Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Sequential operating programs and data which instruct the functioning of a digital computer.
Lipids, predominantly phospholipids, cholesterol and small amounts of glycolipids found in membranes including cellular and intracellular membranes. These lipids may be arranged in bilayers in the membranes with integral proteins between the layers and peripheral proteins attached to the outside. Membrane lipids are required for active transport, several enzymatic activities and membrane formation.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A cyclodecane isolated from the bark of the Pacific yew tree, TAXUS BREVIFOLIA. It stabilizes MICROTUBULES in their polymerized form leading to cell death.
Databases devoted to knowledge about specific genes and gene products.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
The provision of monetary resources including money or capital and credit; obtaining or furnishing money or capital for a purchase or enterprise and the funds so obtained. (From Random House Unabridged Dictionary, 2d ed.)
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Transplantation between individuals of the same species. Usually refers to genetically disparate individuals in contradistinction to isogeneic transplantation for genetically identical individuals.
Transfer of HEMATOPOIETIC STEM CELLS from BONE MARROW or BLOOD between individuals within the same species (TRANSPLANTATION, HOMOLOGOUS) or transfer within the same individual (TRANSPLANTATION, AUTOLOGOUS). Hematopoietic stem cell transplantation has been used as an alternative to BONE MARROW TRANSPLANTATION in the treatment of a variety of neoplasms.
A telecommunication system combining the transmission of a document scanned at a transmitter, its reconstruction at a receiving station, and its duplication there by a copier.
An abnormal congenital condition, associated with defects in the LAMIN TYPE A gene, which is characterized by premature aging in children, where all the changes of cell senescence occur. It is manifested by premature greying; hair loss; hearing loss (DEAFNESS); cataracts (CATARACT); ARTHRITIS; OSTEOPOROSIS; DIABETES MELLITUS; atrophy of subcutaneous fat; skeletal hypoplasia; elevated urinary HYALURONIC ACID; and accelerated ATHEROSCLEROSIS. Many affected individuals develop malignant tumors, especially SARCOMA.
Computers whose input, output and state transitions are carried out by biochemical interactions and reactions.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
A continuous protein fiber consisting primarily of FIBROINS. It is synthesized by a variety of INSECTS and ARACHNIDS.
Substances and materials manufactured for use in various technologies and industries and for domestic use.
Fibrous proteins secreted by INSECTS and SPIDERS. Generally, the term refers to silkworm fibroin secreted by the silk gland cells of SILKWORMS, Bombyx mori. Spider fibroins are called spidroins or dragline silk fibroins.
Formal voluntary or governmental procedures and standards required of hospitals and health or other facilities to improve operating efficiency, and for the protection of the consumer.
An agency of the PUBLIC HEALTH SERVICE concerned with the overall planning, promoting, and administering of programs pertaining to maintaining standards of quality of foods, drugs, therapeutic devices, etc.
Substances intended to be applied to the human body for cleansing, beautifying, promoting attractiveness, or altering the appearance without affecting the body's structure or functions. Included in this definition are skin creams, lotions, perfumes, lipsticks, fingernail polishes, eye and facial makeup preparations, permanent waves, hair colors, toothpastes, and deodorants, as well as any material intended for use as a component of a cosmetic product. (U.S. Food & Drug Administration Center for Food Safety & Applied Nutrition Office of Cosmetics Fact Sheet (web page) Feb 1995)
An application that must be submitted to a regulatory agency (the FDA in the United States) before a drug can be studied in humans. This application includes results of previous experiments; how, where, and by whom the new studies will be conducted; the chemical structure of the compound; how it is thought to work in the body; any toxic effects found in animal studies; and how the compound is manufactured. (From the "New Medicines in Development" Series produced by the Pharmaceutical Manufacturers Association and published irregularly.)
A single-pass type I membrane protein. It is cleaved by AMYLOID PRECURSOR PROTEIN SECRETASES to produce peptides of varying amino acid lengths. A 39-42 amino acid peptide, AMYLOID BETA-PEPTIDES is a principal component of the extracellular amyloid in SENILE PLAQUES.
A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease.
The coordination of services in one area of a facility to improve efficiency.
Endopeptidases that are specific for AMYLOID PROTEIN PRECURSOR. Three secretase subtypes referred to as alpha, beta, and gamma have been identified based upon the region of amyloid protein precursor they cleave.
Peptides generated from AMYLOID BETA-PEPTIDES PRECURSOR. An amyloid fibrillar form of these peptides is the major component of amyloid plaques found in individuals with Alzheimer's disease and in aged individuals with trisomy 21 (DOWN SYNDROME). The peptide is found predominantly in the nervous system, but there have been reports of its presence in non-neural tissue.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A degenerative disease of the BRAIN characterized by the insidious onset of DEMENTIA. Impairment of MEMORY, judgment, attention span, and problem solving skills are followed by severe APRAXIAS and a global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy and the triad of SENILE PLAQUES; NEUROFIBRILLARY TANGLES; and NEUROPIL THREADS. (From Adams et al., Principles of Neurology, 6th ed, pp1049-57)
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
A specified list of terms with a fixed and unalterable meaning, and from which a selection is made when CATALOGING; ABSTRACTING AND INDEXING; or searching BOOKS; JOURNALS AS TOPIC; and other documents. The control is intended to avoid the scattering of related subjects under different headings (SUBJECT HEADINGS). The list may be altered or extended only by the publisher or issuing agency. (From Harrod's Librarians' Glossary, 7th ed, p163)
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
The protein complement of an organism coded for by its genome.

mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. (1/5719)

BACKGROUND: The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis. However, a crystal structure is not available and cap 0 MTases are too diverged from other MTases of known structure to allow straightforward homology-based interpretation of these data. RESULTS: We report a 3D model of cap 0 MTase, developed using sequence-to-structure threading and comparative modeling based on coordinates of the glycine N-methyltransferase. Analysis of the predicted structural features in the phylogenetic context of the cap 0 MTase family allows us to rationalize most of the experimental data available and to propose potential binding sites. We identified a case of correlated mutations in the cofactor-binding site of viral MTases that may be important for the rational drug design. Furthermore, database searches and phylogenetic analysis revealed a novel subfamily of hypothetical MTases from plants, distinct from "orthodox" cap 0 MTases. CONCLUSIONS: Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase. Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases.  (+info)

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. (2/5719)

Proteomics, or the direct analysis of the expressed protein components of a cell, is critical to our understanding of cellular biological processes in normal and diseased tissue. A key requirement for its success is the ability to identify proteins in complex mixtures. Recent technological advances in tandem mass spectrometry has made it the method of choice for high-throughput identification of proteins. Unfortunately, the software for unambiguously identifying peptide sequences has not kept pace with the recent hardware improvements in mass spectrometry instruments. Critical for reliable high-throughput protein identification, scoring functions evaluate the quality of a match between experimental spectra and a database peptide. Current scoring function technology relies heavily on ad-hoc parameterization and manual curation by experienced mass spectrometrists. In this work, we propose a two-stage stochastic model for the observed MS/MS spectrum, given a peptide. Our model explicitly incorporates fragment ion probabilities, noisy spectra, and instrument measurement error. We describe how to compute this probability based score efficiently, using a dynamic programming technique. A prototype implementation demonstrates the effectiveness of the model.  (+info)

An insight into domain combinations. (3/5719)

Domains are the building blocks of all globular proteins, and are units of compact three-dimensional structure as well as evolutionary units. There is a limited repertoire of domain families, so that these domain families are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products. The processes that produce new genes are duplication and recombination as well as gene fusion and fission. We attempt to gain an overview of these processes by studying the structural domains in the proteins of seven genomes from the three kingdoms of life: Eubacteria, Archaea and Eukaryota. We use here the domain and superfamily definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 624 out of the 764 superfamilies in SCOP in these genomes, and the 624 families occur in 585 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour. This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics.  (+info)

Generating protein interaction maps from incomplete data: application to fold assignment. (4/5719)

MOTIVATION: We present a framework to generate comprehensive overviews of protein-protein interactions. In the post-genomic view of cellular function, each biological entity is seen in the context of a complex network of interactions. Accordingly, we model functional space by representing protein-protein-interaction data as undirected graphs. We suggest a general approach to generate interaction maps of cellular networks in the presence of huge amounts of fragmented and incomplete data, and to derive representations of large networks which hide clutter while keeping the essential architecture of the interaction space. This is achieved by contracting the graphs according to domain-specific hierarchical classifications. The key concept here is the notion of induced interaction, which allows the integration, comparison and analysis of interaction data from different sources and different organisms at a given level of abstraction. RESULTS: We apply this approach to compute the overlap between the DIP compendium of interaction data and a dataset of yeast two-hybrid experiments. The architecture of this network is scale-free, as frequently seen in biological networks, and this property persists through many levels of abstraction. Connections in the network can be projected downwards from higher levels of abstraction down to the level of individual proteins. As an example, we describe an algorithm for fold assignment by network context. This method currently predicts protein folds at 30% accuracy without any requirement of detectable sequence similarity of the query protein to a protein of known structure. We used this algorithm to compile a list of structural assignments for previously unassigned genes from yeast. Finally we discuss ways forward to use interaction networks for the prediction of novel protein-protein interactions. AVAILABILITY: http://www.ebi.ac.uk/~lappe/FoldPred/.  (+info)

Prediction of the coupling specificity of G protein coupled receptors to their G proteins. (5/5719)

G protein coupled receptors (GPCRs) are found in great numbers in most eukaryotic genomes. They are responsible for sensing a staggering variety of structurally diverse ligands, with their activation resulting in the initiation of a variety of cellular signalling cascades. The physiological response that is observed following receptor activation is governed by the guanine nucleotide-binding proteins (G proteins) to which a particular receptor chooses to couple. Previous investigations have demonstrated that the specificity of the receptor-G protein interaction is governed by the intracellular domains of the receptor. Despite many studies it has proven very difficult to predict de novo, from the receptor sequence alone, the G proteins to which a GPCR is most likely to couple. We have used a data-mining approach, combining pattern discovery with membrane topology prediction, to find patterns of amino acid residues in the intracellular domains of GPCR sequences that are specific for coupling to a particular functional class of G proteins. A prediction system was then built, being based upon these discovered patterns. We can report this approach was successful in the prediction of G protein coupling specificity of unknown sequences. Such predictions should be of great use in providing in silico characterisation of newly cloned receptor sequences and for improving the annotation of GPCRs stored in protein sequence databases. AVAILABILITY: http://www.ebi.ac.uk/~croning/coupling.html.  (+info)

Non-symmetric score matrices and the detection of homologous transmembrane proteins. (6/5719)

Given a transmembrane protein, we wish to find related ones by a database search. Due to the strongly hydrophobic amino acid composition of transmembrane domains, suboptimal results are obtained when general-purpose scoring matrices such as BLOSUM are used. Recently, a transmembrane-specific score matrix called PHAT was shown to perform much better than BLOSUM. In this article, we derive a transmembrane score matrix family, called SLIM, which has several distinguishing features. In contrast to currently used matrices, SLIM is non-symmetric. The asymmetry arises because different background compositions are assumed for the transmembrane query and the unknown database sequences. We describe the mathematical model behind SLIM in detail and show that SLIM outperforms PHAT both on simulated data and in a realistic setting. Since non-symmetric score matrices are a new concept in database search methods, we discuss some important theoretical and practical issues.  (+info)

Improved prediction of the number of residue contacts in proteins by recurrent neural networks. (7/5719)

Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an ensemble of bi-directional recurrent neural network architectures and evolutionary information to improve the state-of-the-art in contact prediction using a large corpus of curated data. The ensemble is used to discriminate between two different states of residue contacts, characterized by a contact number higher or lower than the average value of the residue distribution. The ensemble achieves performances ranging from 70.1% to 73.1% depending on the radius adopted to discriminate contacts (6Ato 12A). These performances represent gains of 15% to 20% over the base line statistical predictors always assigning an aminoacid to the most numerous state, 3% to 7% better than any previous method. Combination of different radius predictors further improves the performance. SERVER: http://promoter.ics.uci.edu/BRNN-PRED/.  (+info)

Protein-protein interaction map inference using interacting domain profile pairs. (8/5719)

A number of predictive methods have been designed to predict protein interaction from sequence or expression data. On the experimental front, however, high-throughput proteomics technologies are starting to yield large volumes of protein-protein interaction data. High-quality experimental protein interaction maps constitute the natural dataset upon which to build interaction predictions. Thus the motivation to develop the first interaction-based protein interaction map prediction algorithm. A technique to predict protein-protein interaction maps across organisms is introduced, the 'interaction-domain pair profile' method. The method uses a high-quality protein interaction map with interaction domain information as input to predict an interaction map in another organism. It combines sequence similarity searches with clustering based on interaction patterns and interaction domain information. We apply this approach to the prediction of an interaction map of Escherichia coli from the recently published interaction map of the human gastric pathogen Helicobacter pylori. Results are compared with predictions of a second inference method based only on full-length protein sequence similarity - the "naive" method. The domain-based method is shown to i) eliminate a significant amount of false-positives of the naive method that are the consequences of multi-domain proteins; ii) increase the sensitivity compared to the naive method by identifying new potential interactions. AVAILABILITY: Contact the authors.  (+info)

Chris Bizon, Andreas Prlic. Calculating All Pairwise Similarities from the RCSB Protein Data Bank: Client/Server Work Distribution on the Open Science Grid,
The average sequence length in UniProtKB/Swiss-Prot is 359 amino acids. The shortest sequence is GWA_SEPOF (P83570): 2 amino acids. The longest sequence is TITIN_MOUSE (A2ASS6): 35213 amino acids. 4. JOURNAL CITATIONS Note: the following citation statistics reflect the number of distinct journal citations. Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2753 4.1 Table of the frequency of journal citations Journals cited 1x: 866 2x: 391 3x: 163 4x: 136 5x: 110 6x: 100 7x: 66 8x: 56 9x: 37 10x: 33 11- 20x: 219 21- 50x: 227 51-100x: 118 ,100x: 231 4.2 List of the most cited journals in UniProtKB/Swiss-Prot Nb Citations Journal name -- --------- ------------------------------------------------------------- 1 24439 Journal of Biological Chemistry 2 11326 Proceedings of the National Academy of Sciences of the U.S.A. 3 6606 Journal of Bacteriology 4 5619 Biochemical and Biophysical Research Communications 5 5312 Biochemistry 6 4984 Nucleic Acids Research 7 4816 FEBS Letters 8 ...
VIEW RECORDING. DOWNLOAD SLIDES. ABSTRACT. I first posed this question in an Editorial in 2005. Well the future is now, so what is the answer to the question? I will give you at least my opinion of an answer and back it up with work that we and others have been doing at this interface. My own experience will be drawn from our database work with the RCSB Protein Data Bank (PDB) and the Immune Epitope Database (IEDB) and as Co-founder and Founding Editor in Chief of the journal PLOS Computational Biology.. SPEAKER BIOGRAPHY. Philip E. Bourne PhD is Associate Vice Chancellor for Innovation and Industry Alliances, a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego, Associate Director of the RCSB Protein Data Bank and an Adjunct Professor at the Sanford Burnham Institute. Bournes professional interests focus on relevant biological and educational outcomes derived from computation and scholarly ...
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for researchers and students interested in structural biology. At its center is the PDB archive -- the sole international repository for the 3-dimensional structure data of biological macromolecules. These structures hold significant promise for the pharmaceutical and biotechnology industries in the search for new drugs and in efforts to understand the mysteries of human disease The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB processes, stores, and disseminates these important data, and develops the software tools needed to assist users in depositing and accessing structural information The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has an opening for a Biochemical Information & Annotation Specialist to curate and standardize macromolecular ...
PDB setzte sich ursprünglich aus Proteinstrukturen aus der Röntgen-Kristallstrukturanalyse und dem 1968 gegründeten Brookhaven RAster Display (BRAD) zusammen. Im Jahr 1969, entstand unter der Förderung durch Walter Hamilton am Brookhaven National Laboratory und der Urheberschaft von Edgar Meyer (Texas A&M University) eine Software zur Speicherung von Atomkoordinaten in einem gemeinsamen Format. Im Jahr 1971 wurde die Suchfunktion SEARCH eingeführt, mit der die Daten heruntergeladen und offline gespeichert werden konnten.[3] Nach Hamiltons Tod 1973 übernahm Tom Koeztle die Leitung für die folgenden 20 Jahre. Im Jahr 1994 ging die Führung an Joel Sussman über. Von Oktober 1998 bis Juni 1999 wurde PDB in das Research Collaboratory for Structural Bioinformatics (RCSB) übertragen.[4][5] Dort wurde Helen M. Berman of Rutgers University neue Direktorin.[6] Im Jahr 2003 wurde PDB mit der Gründung von Worldwide Protein Data Bank (wwPDB) international. Gründungsmitglieder sind PDBe ...
The RCSB web servers returned an unexpected error. It has been logged and will be reviewed by the PDB team. Here are some suggested remedial steps: ...
The RCSB web servers returned an unexpected error. It has been logged and will be reviewed by the PDB team. Here are some suggested remedial steps: ...
The Data Catalogue is a service that allows University of Liverpool Researchers to create records of information about their finalised research data, and save those data in a secure online environment. The Data Catalogue provides a good means of making that data available in a structured way, in a form that can be discovered by both general search engines and academic search tools. There are two types of record that can be created in the Data Catalogue: A discovery-only record - in these cases, the research data may be held somewhere else but a record is provided to help people find it. A record is created that alerts users to the existence of the data, and provides a link to where those data are held. A discovery and data record - in these cases, a record is created to help people discover the data exist, and the data themselves are deposited into the Data Catalogue. This process creates a unique Digital Object identifier (DOI) which can be used in citations to the data ...
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12922 The first twenty species represent 112553 sequences: 20.9 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5426 2x: 1882 3x: 981 4x: 639 5x: 466 6x: 381 7x: 284 8x: 217 9x: 199 10x: 123 11- 20x: 668 21- 50x: 403 51-100x: 212 ,100x: 1041 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20233 Homo sapiens (Human) 2 16566 Mus musculus (Mouse) 3 11571 Arabidopsis thaliana (Mouse-ear cress) 4 7815 Rattus norvegicus (Rat) 5 6621 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) 6 5965 Bos taurus (Bovine) 7 5089 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4188 Bacillus subtilis (strain 168) 10 4126 Dictyostelium ...
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12726 The first twenty species represent 111314 sequences: 20.8 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5365 2x: 1849 3x: 955 4x: 628 5x: 463 6x: 374 7x: 272 8x: 218 9x: 198 10x: 110 11- 20x: 655 21- 50x: 392 51-100x: 209 ,100x: 1038 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20246 Homo sapiens (Human) 2 16473 Mus musculus (Mouse) 3 11018 Arabidopsis thaliana (Mouse-ear cress) 4 7690 Rattus norvegicus (Rat) 5 6619 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) 6 5885 Bos taurus (Bovine) 7 4976 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4244 Bacillus subtilis 10 4122 Dictyostelium discoideum (Slime ...
Thus, for the same protein, different sets of binding-site residues might be obtained depending on the PDB structure that is considered, and a residue of a protein may be defined as binding-site residue in one PDB structure but as non-binding-site residue in another. This inconsistency can cause serious problems in research. Thus, for a given protein, researchers need to identify all PDB structures that contain the protein, and calculate binding-site residues on the protein using all of them.. After users have found all the PDB structures that contain a given protein, the protein sequences shown in different PDB structures must be aligned properly to combine the binding-site information obtained from different structures. This step is not as simple as it may first appear. It cannot be done by matching the sequence indexes of residues in the PDB structures, because the same protein chain may have different sequence indexing in different PDB structures. For example, 1qqi_A and 1gxp_A are the same ...
Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative pepti
An improved multistage intelligent database search method includes (1) a prefilter that uses a precomputed index to compute a list of most
The table below provides information about proteins whose structures have been determined by solid-state NMR, to a resolution sufficient to have resulted in a file deposited with the worldwide Protein Data Bank (wwPDB). Here is the NMR page of the wwPDB ...
Accession numbers must be cited immediately following the Materials and Methods section. Accession numbers are unique identifiers in bioinformatics allocated to nucleotide and protein sequences to allow tracking of different versions of that sequence record and the associated sequence in a data repository [e.g., databases at the National Center for Biotechnical Information (NCBI) at the National Library of Medicine (GenBank) and the Worldwide Protein Data Bank]. There are different types of accession numbers in use based on the type of sequence cited, each of which uses a different coding. Authors should explicitly mention the type of accession number together with the actual number, bearing in mind that an error in a letter or number can result in a dead link in the online version of the article. Please use the following format: accession number type ID: xxxx (e.g., MMDB ID: 12345; PDB ID: 1TUP). Note that in the final version of the electronic copy, accession numbers will be linked to the ...
Are you a structural biologist looking for an exciting career change in 2016?. We are looking to recruit an expert structural biologist (with experience in structure determination) to join the Protein Data Bank in Europe curation team (PDBe: pdbe.org) at the European Bioinformatics Institute (EMBL-EBI, Cambridge, UK: ebi.ac.uk) as a Scientific Data Curator. The work involves annotating preliminary PDB and Electron Microscopy Data Bank (EMDB) submissions and extracting relevant biological information. In addition, curators contribute to training, outreach and user-support activities of PDBe and the EMBL-EBI.. For more information, please go to:. https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54423&aid=15470. ...
Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G. Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61. doi: 10.1093/nar/gkr930. Epub 2011 Nov 16. ...
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are ...
The Protein Identifier Mapping Service provides a free interface to resolve protein identifiers across multiple databases that correspond to the same logical protein.
DNA-binding pseudobarrel domain superfamily domain assignments in TargetDB . Domain assignment details for each protein include region, Evalue and model. Alignments, domain architectures and domain combinations are provided for each group of proteins.
Protein structure mining using a structural alphabet.: Protein structure mining using a structural alphabet. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Biomedical applications drive all aspects of our methods development efforts. We do this through collaborations with biomedical scientists, and through primary biomedical research within the CCSB. We also have a strong commitment to biomedical education and outreach, using CCSB tools to disseminate the results of biomedical research to diverse audiences.. As part of the HIVE Center, we are studying HIV and its interaction with host cells throughout the viral life cycle.. In collaboration with Barry Sharpless, we are designing specific covalent inhibitors and applying them to multiple biomedical targets.. Working with PDB-101, the outreach/education portal of the RCSB Protein Data Bank, we produce many materials and resources for use in education and outreach.. ...
Figure 1. Above is a Jmol image of the consensus V3 loop of gp120. The partially-hidden nature of the conserved region of gp120 makes it difficult for our bodies to develope effective neutralizing antibodies. The image is from the RCSB Protein Data Bank. PDB 1CE4. Antibodies specific to gp120 and the gp41 envelope proteins (Janeway et al, 2005) can be found in plasma of infected patients within weeks of initial infection (Paul, 2003), and may play a role in minimizing viral impact during the asymptomatic period, but are unable to clear an infection. Despite the early presence of HIV-specific antibodies, the high levels of antibodies with the ability to neutralize viruses are generally only found in long-term nonprogressors (Paul, 2003). Two trimers of gp120 and gp41 create the envelope protein gp160, which is heavily glycosylated. CD4 T cells bind gp120 on a depression in the protein (Paul, 2003). The virus also binds chemokine receptors on another depressed site on gp120 as co-receptors. Both ...
Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are ...
There are 330 cases currently listed in Australia. Results are displayed 25 per page. Login or create an account for additional advocacy tools, including e-mail notifications when updates are posted to selected cases.. Pages: 1 2 3 4 5 6 7 8 9 10 Next» ...
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InterPro is an integrated resource for protein families, domains, and active sites. The resource provides an invaluable means for automatic classification of protein sequences into families or domains with a view to providing functional annotation for the proteins. It constitutes an amalgamation of the major protein signature databases: PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR SuperFamily, and SUPERFAMILY into a unified database where similarities and differences between the signatures from each of these databases are rationalized for ease of use. All signatures representing the same family or domain are collated into unique InterPro entries, with annotation and a list of the proteins in UniProt that these signatures match. New sequences not available in UniProt can be run through all signatures in InterPro using the InterProScan software. InterPro is useful for large-scale classification of whole genomes, as well as for functional annotation of individual protein sequences. ...
PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), CharProtDB, MetaCyc, EcoCyc, REBASE, and the Fitness Browser. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E , 0.001. To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form locus_tag AND genus_name to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears ...
Tutor: Micaela Lewinson. Bioinformatics is an interdisciplinary area of study linking computational tools and databases to biology. Topics such as DNA sequence analysis, genome sequencing, expression of genes, 3D-structures of proteins are all considered parts of bioinformatics. In my Bioinformatics course (BIO 260) students are introduced to this exciting new interdisciplinary area spanning computational science and biology. This is a non-traditional biology course - it does not have a wet lab, but students spend a significant time in the computer lab using various databases (such as DNA sequence databases, protein structure databases) and software packages to solve problems in biology. One of the class projects is analysis and annotation of a previously unpublished, newly sequenced genome. Through this project students have an opportunity to use digital research to make a novel contribution to science! This exciting project is made possible through my participation in a multi-institution ...
ARLINGTON Va.- The assets of the Protein Data Bank (PDB) justkeep ...The PDB holds the three-dimensional structures of nearly 24000p...This month with a doubling in the number of the federal agencies...Mary Clutter assistant director for NSFs Directorate forBiolog... Biological processes involve small molecular machines shesaid...,Protein,data,bank,opens,new,era,with,broader,support,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
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Using a number of diverse protein families as test cases, we investigate the ability of the recently developed iterative sequence database search method, PSI-BLAST, to identify subtle relationships between proteins that originally have been deemed detectable only at the level of structure-structure comparison. We show that PSI-BLAST can detect many, though not all, of such relationships, but the success critically depends on the optimal choice of the query sequence used to initiate the search. Generally, there is a correlation between the diversity of the sequences detected in the first pass of database screening and the ability of a given query to detect subtle relationships in subsequent iterations. Accordingly, a thorough analysis of protein superfamilies at the sequence level is necessary in order to maximize the chances of gleaning non-trivial structural and functional inferences, as opposed to a single search, initiated, for example, with the sequence of a protein whose structure is ...
Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s ...
Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s ...
08h30 Protein sequence databases: theory. 10h30 COFFEE BREAK. 11h00 Controlled vocabularies and standardization resources: theory. 12h15 LUNCH. 13h30 Protein sequence databases and Gene Ontology: practicals. 15h00 COFFEE BREAK. 15h30 Analysis tools using ontologies : theory. 16h00 Protein sequence databases and Gene Ontology: practicals. 17h00 Evaluation / Exam. 18h00 END ...
RGD:2851, RGD:2850, FB:FBgn0087012, MGI:MGI:109323, UniProtKB:P28335, UniProtKB:P30939, UniProtKB:O46635, UniProtKB:P08908, FB:FBgn0263116, FB:FBgn0004168, MGI:MGI:96274, MGI:MGI:96276, MGI:MGI:96273, UniProtKB:P41595, PANTHER:PTN000664111, UniProtKB:P47898, RGD:61800, UniProtKB:A0A0B4KFU6, UniProtKB:P28566, UniProtKB:Q13639, UniProtKB:P28222, UniProtKB:P28223, UniProtKB:Q50DZ8, UniProtKB:P28221, RGD:71034, FB:FBgn0004573, MGI:MGI:96281, MGI:MGI:96284, WB:WBGene00004776, RGD:2848, RGD:62044, RGD:62388, WB:WBGene00004779, RGD:2846, RGD: ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAS …
TY - JOUR. T1 - A top-down approach to infer and compare domain-domain interactions across eight model organisms. AU - Guda, Chittibabu. AU - King, Brian R.. AU - Pal, Lipika R.. AU - Guda, Purnima. PY - 2009/3/31. Y1 - 2009/3/31. N2 - Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer functionally relevant DDIs from PPI data. We created a comprehensive, non-redundant dataset of 209,165 experimentally-derived PPIs by combining datasets from five major interaction databases. We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting ...
Recombinant DNA technology has been extensively employed to generate a variety of products from genetically modified organisms (GMOs) over the last decade, and the development of technologies capable of analyzing these products is crucial to understanding gene expression patterns. Liquid chromatography coupled with mass spectrometry is a powerful tool for analyzing protein contents and possible expression modifications in GMOs. Specifically, the NanoUPLC-MSE technique provides rapid protein analyses of complex mixtures with supported steps for high sample throughput, identification and quantization using low sample quantities with outstanding repeatability. Here, we present an assessment of the peptide and protein identification and quantification of soybean seed EMBRAPA BR16 cultivar contents using NanoUPLC-MSE and provide a comparison to the theoretical tryptic digestion of soybean sequences from Uniprot database. The NanoUPLC-MSE peptide analysis resulted in 3,400 identified peptides, 58% of which
The problem: There are far too many proteins for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence (and all other data one can find). At the same time, how can we judge how well these function prediction algorithms are performing and whether we are making progress over time?. The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function, Biological Process, and Cellular Component. In addition, predictors may use the Human Phenotype Ontology (HPO) for the human dataset. A set of protein sequences is provided by the organizers, and participants are expected to submit ...
There is a frequent need to obtain sets of functionally equivalent homologous proteins (FEPs) from different species. While it is usually the case that orthology implies functional equivalence, this is not always true; therefore datasets of orthologous proteins are not appropriate. The information relevant to extracting FEPs is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEPs to be extracted on a one-off basis. However there has been no resource allowing the easy, automatic extraction of groups of FEPs - for example, all instances of protein C. We have developed FOSTA, an automatically generated database of FEPs annotated as having the same function in UniProtKB/Swiss-Prot which can be used for large-scale analysis. The method builds a candidate list of homologues and filters out functionally diverged proteins on the basis of functional annotations using a simple text mining approach. Large scale evaluation of our FEP extraction method is difficult as
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SDAP (Structural Database of Allergenic Proteins) is a Web server that provides database information and various cobputational tools for the study of allergenic proteins. The database component of SDAP contains information the allergen name, source, sequence, structure, IgE epitopes, and literature references, and links to the major protein (PDB, SWISS-PROT, PIR, NCBI) and literature (PubMed, MEDLINE) servers. The computational component in SDAP uses an original algorithm based on conserved properties of amino acid side chains to identify regions of known allergens similar to user-supplied peptides or selected from the SDAP database of IgE epitopes. This and other bioinformatics tools can be used to rapidly determine potential cross-reactivities between allergens and to screen novel proteins for the presence of IgE epitopes they may share with known allergens. SDAP was developed guided by the allergens list from the IUIS (International Union of Immunological Societies) website, ...
Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. glyco, disulf bond, Signal peptide etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.. Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic. In the UniProt Modifications track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.. Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same ...
Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. glyco, disulf bond, Signal peptide etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.. Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic. In the UniProt Modifications track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.. Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same ...
The Protein Data Bank archive (PDB) is a worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, managed by the Worldwide PDB (wwPDB). The PDB Exchange Dictionary (PDBx) is used by the wwPDB to define data content for deposition, annotation and archiving of PDB entries. PDBx incorporates the community standard metadata representation, the Macromolecular Crystallographic Information Framework (mmCIF), orginally developed under the auspices of the International Union of Crystallography (IUCr). PDBx has been extended by the wwPDB to include descriptions of other experimental methods that produce 3D macromolecular structure models such as Nuclear Magnetic Resonance Spectroscopy, 3D Electron Microscopy and Tomography. ...
The Cambridge Structural Database (CSD) is a highly curated and comprehensive resource.. Established in 1965, the CSD is the worlds repository for small-molecule organic and metal-organic crystal structures. Containing over 900,000 entries from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.. With comprehensive and fully retrospective coverage of the published literature you can have full confidence that your CSD searches are returning all crystal structure matches. The CSD also contains data published directly through the CSD as CSD Communications that are not available anywhere else.. ...
CP000667.PE356 Location/Qualifiers FT CDS 407150..408517 FT /codon_start=1 FT /transl_table=11 FT /locus_tag=Strop_0356 FT /product=glutamyl-tRNA reductase FT /EC_number=1.2.1.70 FT /note=PFAM: glutamyl-tRNA reductase; Shikimate/quinate FT 5-dehydrogenase FT /db_xref=EnsemblGenomes-Gn:Strop_0356 FT /db_xref=EnsemblGenomes-Tr:ABP52841 FT /db_xref=GOA:A4X1U1 FT /db_xref=InterPro:IPR000343 FT /db_xref=InterPro:IPR006151 FT /db_xref=InterPro:IPR015895 FT /db_xref=InterPro:IPR015896 FT /db_xref=InterPro:IPR036291 FT /db_xref=InterPro:IPR036343 FT /db_xref=InterPro:IPR036453 FT /db_xref=UniProtKB/Swiss-Prot:A4X1U1 FT /protein_id=ABP52841.1 FT /translation=MKLLVVGASYRTAPVAALERLTVAPADLSRVLTRLVAQPYVSEAV FT LVSTCNRVEVYAVVSGFHGGLGDICAVLAESTGCQPAALADHLYVHFDAAAVNHVFRVA FT VGLDSMVVGEAQILGQLRDAYHWASEAETVGRLLHELMQQALRVGKRAHSETGIDRAGQ FT SVVTAALGLATELLHSDLACRPALVVGAGAMGSLGVATLARLGAGPVSVTNRGVDRAIR FT LAESYGATAVPIADLTATLSTVDIVVAATAAPEAVLTRAVVTQALAGRNPSRGPLVLLD FT ...
Many journals impose guidelines for the reporting of database search results, designed to ensure that the data are reliable. This was initiated by the Editors of Molecular and Cellular Proteomics, who organised a workshop in 2005 to discuss the issues, culminating in the Paris Guidelines. The current guidelines require For large scale experiments, the results of any additional statistical analyses that estimate a measure of identification certainty for the dataset, or allow a determination of the false discovery rate, e.g., the results of decoy searches or other computational approaches.. This is a recommendation to repeat the search, using identical search parameters, against a database in which the sequences have been reversed or randomised. You do not expect to get any true matches from the decoy database. So, the number of matches that are found is an excellent estimate of the number of false positives that are present in the results from the real or target database. This approach ...
GENEID ONLINE SYSTEM FOR PREDICTION OF GENE STRUCTURE version 1.1 3/1/1993 ______________________________________________________________________ The GeneID server, which was first brought online at geneid at darwin.bu.edu in December 1991, has now had a few enhancements added: 1. It is now available at geneid at bir.cedb.uwf.edu as well. 2. Predicted gene models are automatically compared to protein databases. 3. Several options can be supplied on the command line (Genomic Sequence): -small_output : Mails only exons and gene models back to user. -all_exons : Allows scanning for exons in small gene fragments. -noblast : Turns off protein database search -netgene : Send the file to netgene as well. Example: Genomic Sequence -noblast -small_output 4. Error handling has been improved to supply a more meaningful feedback to the user, and be a little less unforgiving of user error. 5. The upper limit in sequence size has been increased from 20,000 bp to 200,000 bp NOTE that all these enhancements ...
Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD) that takes into account the organization of the domains into hierarchies of homologous domain models. Our analysis of alignment scores from NCBI-curated domain assignments suggests that identifying the correct model among closely related models is more difficult than choosing between non-overlapping domain models. We find that simple heuristics based on sorting scores and domain-specific thresholds are effective at reducing classification error. In fact, in our test set, the heuristics result in almost 90% of current misclassifications due to missing domain subfamilies being replaced by more generic domain
ID NIRB_ECOLI Reviewed; 847 AA. AC P08201; Q2M731; DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1995, sequence version 4. DT 25-OCT-2017, entry version 161. DE RecName: Full=Nitrite reductase (NADH) large subunit; DE EC=1.7.1.15; GN Name=nirB; OrderedLocusNames=b3365, JW3328; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RX PubMed=2543955; DOI=10.1093/nar/17.10.3865; RA Bell A.I., Gaston K.L., Cole J.A., Busby S.J.W.; RT Cloning of binding sequences for the Escherichia coli transcription RT activators, FNR and CRP: location of bases involved in discrimination RT between FNR and CRP.; RL Nucleic Acids Res. 17:3865-3874(1989). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RX PubMed=2200672; DOI=10.1111/j.1432-1033.1990.tb19125.x; RA Peakman T., Crouzet J., Mayaux J.F., Busby S.J.W., Mohan S., ...
AL009126.MCSB Location/Qualifiers FT CDS 102484..103575 FT /codon_start=1 FT /transl_table=11 FT /gene=mcsB FT /locus_tag=BSU_00850 FT /old_locus_tag=BSU00850 FT /product=protein arginine kinase FT /function=16.3: Control FT /EC_number=2.7.3.3 FT /note=Evidence 1a: Function from experimental evidences in FT the studied strain; PubMedId: 16163393, 17380125, 19189946, FT 21622759, 25610436, 27749819; Product type e : enzyme FT /db_xref=EnsemblGenomes-Gn:BSU00850 FT /db_xref=EnsemblGenomes-Tr:CAB11861 FT /db_xref=GOA:P37570 FT /db_xref=InterPro:IPR000749 FT /db_xref=InterPro:IPR014746 FT /db_xref=InterPro:IPR022414 FT /db_xref=InterPro:IPR022415 FT /db_xref=InterPro:IPR023660 FT /db_xref=SubtiList:BG10147 FT /db_xref=UniProtKB/Swiss-Prot:P37570 FT /experiment=publication(s) with functional evidences, FT PMID:16163393, 17380125, 19189946, 21622759, 25610436, FT 27749819 FT /protein_id=CAB11861.1 FT /translation=MSLKHFIQDALSSWMKQKGPESDIVLSSRIRLARNFEHIRFPTRY FT ...
Protein 3D structures are currently determined experimentally via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The process is slow (it can take weeks or even months to figure out how to crystallize a protein for the first time) and costly (around US$100,000 per protein).[15] Unfortunately, the rate at which new sequences are discovered far exceeds the rate of structure determination - out of more than 7,400,000 protein sequences available in the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database, fewer than 52,000 proteins 3D structures have been solved and deposited in the Protein Data Bank, the main repository for structural information on proteins.[16] One of the main goals of [email protected] is to predict protein structures with the same accuracy as existing methods, but in a way that requires significantly less time and money. [email protected] also develops methods to determine the structure and docking of membrane proteins (e.g., G ...
MedAI, provides customers with professional prediction of protein-protein interaction solutions according to their detailed requirements.
ESPRIT: Screening of tens of thousands of constructs of a single gene to identify well-behaving soluble constructs. Academic structural biologists often work on proteins that lack accurate domain annotations. When the full-length protein cannot be expressed and a domain-focused approach is necessary, problems arise since it is unclear how to design high yielding, soluble expression constructs. Some proteins have little or no sequence similarity to others and this prevents domain identification using multiple sequence alignments. More often, some functional annotation exists e.g. from mutagenesis or deletion studies, but these regions do not define well the structural boundaries. Even when a soluble construct is obtained, disordered extensions may confound crystallisation attempts. We are all familiar with these situations; in many cases they are what keep our proteins hot and out of the PDB.. The ESPRIT technology was developed in the Hart lab at EMBL to express proteins whose domain ...
The SCOP classification for the S13-like H2TH domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
The SCOP classification for the XPC-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
The SCOP classification for the ISP domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
File: ID Symbol Taxon Taxon Name Evidence GO ID GO Name + Aspect Reference With Source H1SXX9 Symbol1 12345 Homo Sapiens IEA GO:0015031 pro +tein transport Process GO_REF:0000002 InterPro:IPR027282 +InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0003824 cat +alytic activity Function GO_REF:0000002 InterPro:IPR003607 + InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0008152 met +abolic process Process GO_REF:0000002 InterPro:IPR002912 +InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0008728 GTP + diphosphokinase activity Function GO_REF:0000003 EC:2.7.6.5 + UniProt H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0015969 gua +nosine tetraphosphate metabolic process Process GO_REF:0000002 + InterPro:IPR004811,InterPro:IPR007685 InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0016301 kin +ase activity Function GO_REF:0000038 UniProtKB-KW:KW-0418 + UniProt H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0016310 pho +sphorylation Process GO_REF:0000038 UniProtKB-KW:KW-0418 +UniProt H1SXZ5 Symbol2 12345 ...
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ID LACI_ECOLI Reviewed; 360 AA. AC P03023; O09196; P71309; Q2MC79; Q47338; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2003, sequence version 3. DT 20-MAR-2007, entry version 87. DE Lactose operon repressor. GN Name=lacI; OrderedLocusNames=b0345, JW0336; OS Escherichia coli. OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=562; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0; RA Farabaugh P.J.; RT Sequence of the lacI gene.; RL Nature 274:765-769(1978). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Chen J., Matthews K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Marsh S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., ...
Predicting the function of an uncharacterized protein is a major challenge in post-genomic era due to problems complexity and scale. Having knowledge of protein function is a crucial link in the...
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Other names in common use include beta-ketoacyl-[acyl-carrier protein](ACP) reductase, beta-ketoacyl acyl carrier protein (ACP ... 3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP+ ⇌. {\displaystyle \rightleftharpoons }. 3-oxoacyl-[acyl-carrier-protein] + ... beta-ketoacyl-acyl carrier protein reductase, 3-ketoacyl acyl carrier protein reductase, 3-ketoacyl ACP reductase, NADPH- ... acylcarrier-protein] dehydrase, and enoyl-[acyl-carrier-protein] reductase from Spinacia oleracea leaves". Arch. Biochem. ...
These families have been documented in dozens of different protein and protein family databases such as Pfam. Enzymes are ... Mulder NJ (28 September 2007). "Protein Family Databases". eLS. Chichester, UK: John Wiley & Sons, Ltd. pp. a0003058.pub2. doi: ... Hunter T (January 1995). "Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling". Cell. ... argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, ...
"The Pfam protein families database". Nucleic Acids Research. 32 (Database issue): 138D-1141. doi:10.1093/nar/gkh121. ISSN 0305- ... In 2003, he introduced the Rfam database of RNA families. He was also involved in providing protein analysis for the ... He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been ... Database. 2012: bar059. doi:10.1093/database/bar059. PMC 3308150. PMID 22434828. Bateman, A; Eddy, S. R.; Chothia, C (1996). " ...
This protein only binds long dsRNAs, but the mechanism producing this length specificity is unknown. This RNA-binding protein ... Database. 2014: bau103. doi:10.1093/database/bau103. PMC 4224276. PMID 25380780. Pillai RS, Bhattacharyya SN, Filipowicz W ( ... This ancestral RNAi system probably contained at least one dicer-like protein, one argonaute, one PIWI protein, and an RNA- ... In fission yeast this complex contains argonaute, a chromodomain protein Chp1, and a protein called Tas3 of unknown function. ...
This is still the meaning of rhodopsin in the narrow sense, any protein evolutionarily homologous to this protein. In a broad ... Database. 2015: bav080. doi:10.1093/database/bav080. PMC 4539915. PMID 26286928. Yawo H, Kandori H, Koizumi A (5 June 2015). ... the native conformation of protein is stabilized in the trimeric protein-bacterioruberin complex. Mutants of Archaerhodopsin-3 ... Most proteins of the MR family are all of about the same size (250-350 amino acyl residues) and possess seven transmembrane ...
Database. 2015: bav112. doi:10.1093/database/bav112. PMC 4669993. PMID 26637529. Levoye A, Dam J, Ayoub MA, Guillaume JL, ... Examples of orphan receptors are found in the G protein-coupled receptor (GPCR) and nuclear receptor families. If an endogenous ... Wise A, Jupe SC, Rees S (2004). "The identification of ligands at orphan G-protein coupled receptors". Annu Rev Pharmacol ... In biochemistry, an orphan receptor is a protein that has a similar structure to other identified receptors but whose ...
Protein Bioinformatics Databases and Resources. Retrieved 26 October 2020. "Neuropeptide W/neuropeptide B receptors , G protein ... Zhang Y, Wang Z, Parks GS, Civelli O (2011). "Novel neuropeptides as ligands of orphan G protein-coupled receptors". Current ... Mazzocchi G, Rebuffat P, Ziolkowska A, Rossi GP, Malendowicz LK, Nussdorfer GG (June 2005). "G protein receptors 7 and 8 are ... January 2003). "Identification of natural ligands for the orphan G protein-coupled receptors GPR7 and GPR8". The Journal of ...
... to 100-fold higher heterologous protein expression levels. These features make P. methanolica very useful as a protein ... 30(2):515 "CABI databases". Retrieved 24 January 2013. Makig. (1974), In: J. gen. appl. Microbiol., Tokyo 20(2):124 http:// ... haploid organism that offers many of the advantages of a eukaryotic expression system such as protein processing and protein ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... The three proteins TRPML1, TRPML2 and TRPML3 are encoded by the mucolipin-1 (MCOLN1), mucolipin-2 (MCOLN2) and mucolipin-3 ( ... "Transient Receptor Potential Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and ... comprises a group of three evolutionarily related proteins that belongs to the large family of transient receptor potential ion ...
"LGR5 leucine-rich repeat containing G protein-coupled receptor 5". IUPHAR Database. Carmon KS, Lin Q, Gong X, Thomas A, Liu Q ( ... is a protein that in humans is encoded by the LGR5 gene. It is a member of GPCR class A receptor proteins. R-spondin proteins ... Leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5) also known as G-protein coupled receptor 49 (GPR49) or G- ... Moreover, R-spondin proteins were shown to interact with the extracellular domain of LRG5. The LGR5 / R-spondin complex acts by ...
Homma, K.S. (2011). "List of autophagy-related proteins and 3D structures". Autophagy Database. 290. Archived from the original ... WIPI2, a PtdIns(3)P binding protein of the WIPI (WD-repeat protein interacting with phosphoinositides) protein family, was ... neurons gather ubiquitinated protein aggregates and degrade.[citation needed] Ubiquitinated proteins are proteins that have ... This allows unneeded proteins to be degraded and the amino acids recycled for the synthesis of proteins that are essential for ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels. Ion Channels at the US ... Ion channels are integral membrane proteins, typically formed as assemblies of several individual proteins. Such "multi-subunit ... Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters. The study of ion channels ... Because of their small size and the difficulty of crystallizing integral membrane proteins for X-ray analysis, it is only very ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... TRPV proteins respond to the taste of garlic (allicin). TRPV1 contributes to heat and inflammation sensations and mediates the ... The name now refers only to a family of proteins with similar structure and function, not to the mechanism of their activation ... TRP channels are a large group of ion channels consisting of six protein families, located mostly on the plasma membrane of ...
"UniProt Database". "Unigene (EST profile viewer) Human C11orf1". "SET domain, bifurcated 1 [Homo sapiens]". Protein. National ... 2005). "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi: ... The human protein SET domain bifurcated 1, was found to be a binding partner for C11orf1 by Yeast Two Hybrid. GRCh38: Ensembl ... "CDD: Conserved Domain Database (NCBI)". Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (March 1992). "Methods and ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... Two other proteins, stromal interaction molecules (STIMs) and Orais, however, have more recently been implicated in this ... IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology. " ... Pathological stress or hypertrophic agonists will trigger G-protein coupled receptors (GPCRs) and activates PLC to form DAG and ...
Potential protein interacting partners for IRX1 were found using computational tools. The STRING database lists nine putative ... Iroquois-class homeodomain protein IRX-1, also known as Iroquois homeobox protein 1, is a protein that in humans is encoded by ... its similarity to an internal region of the Notch receptor protein suggests that it may be involved with protein-protein ... The mature IRX1 protein has 480 amino acid residues, with a molecular mass of 49,600 Daltons and an isoelectric point of 5.7. A ...
... is in the protein family that contains ankyrin-repeat domains. Ankyrin repeats are known for mediating protein-protein ... "mint database". mint.bio.uniroma2.it. Archived from the original on 2006-05-06. Retrieved 2016-04-24. "STRING: functional ... The protein's function in humans is currently unknown. ANKRD24 is in the protein family that contains ankyrin-repeat domains. ... The protein does not have any significant negative charge clusters and no significant charge patterns. The ANKRD24 protein is ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... TRPM6 and TRPM7, for example, contain functional α-kinase segments, which are a type of serine/threonine-specific protein ... IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology. " ... contain entire functional proteins in their C-termini. ...
... is the largest of the four proteins. Bartonella henselae: BH11960. KEGG Database. [2]. Aslmark, C.M., et al. 2004. The ... "Hypothetical protein BH11960 (Bartonella henselaei str. Houston-1". [1]. The function of the BH11960 protein is not known, but ... Bartonella henselae hypothetical protein 11960 (BH11960) is encoded by the BH11960 gene. This hypothetical protein is conserved ... Furthermore, a signal peptide protein is present in this region that allows transport of a protein. Based on sequence analysis ...
"Phyre2 Database". Phyre2. "SOPMA secondary prediction". "GOR protein prediction". "I-TASSER results". zhanglab.ccmb.med.umich. ... The protein has an isoelectric point (pI) of 11. The predicted molecular weight (mW) is 160kDa for the human protein, but ... The protein is 1468 amino acids in length with a molecular weight of 162.42 kDa. The mRNA sequence was found to be 4689 base ... "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-04-22. "CFSSP: Chou & Fasman Secondary Structure ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... Here, its activity is decreased and it suppresses the activation of G proteins by PKD1. Group 1: polycystic kidney disease 1 ( ... PKD1) like proteins PKD1 PKD1 PKDREJ PKD1L1 PKD1L2 PKD1L3 Group 2: polycystic kidney disease 2 (PKD2) like proteins TRPP1 PKD2 ... "Transient Receptor Potential Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and ...
"TMEM229B Gene - GeneCards , T229B Protein T229B Antibody". GeneCards V3 - Human Genes , Gene Database. Retrieved 2011-04-19. ... Transmembrane protein 229b is a protein that in humans is encoded by the TMEM229b gene. The TMEM229B gene is also known as ... The translated TMEM229B protein is a total of 167 amino acids long, with a predicted molecular weight of 19,531 Daltons. The ... Annotated diagram of the TMEM229b gene (with its 3 exons), mature mRNA and protein domains. Functional peptide is predicted to ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels.. ... The identity of the mutated protein was unknown until it was cloned by Craig Montell, a post-doctoral researcher in Gerald ... PKD1-like genes encode much larger proteins with 11 transmembrane segments, which do not have all the features of other TRP ... The ion selectivity filter, pore, is formed by the complex combination of p-loops in the tetrameric protein, which are situated ...
"TRIP Database". a manually curated database of protein-protein interactions for mammalian TRP channels. Calcium+Channels at the ... ISBN 978-0-443-07145-4. "TPCN1 - Two pore calcium channel protein 1 - Homo sapiens (Human) - TPCN1 gene & protein". www.uniprot ... "Voltage-Gated Ion Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical ...
Database, GeneCards. "WDR90 Gene - GeneCards , WDR90 Protein , WDR90 Antibody". www.genecards.org. Retrieved 2015-05-06. CS1 ... WD repeat-containing protein 90 is a protein that in humans is encoded by the WDR90 gene (16p13.3). This human protein is 1750 ... its ties to the protein superfamily WD40 domain-containing proteins, and the known protein interactions, it could play a role ... Database, GeneCards. "WDR16 Gene - GeneCards , WDR16 Protein , WDR16 Antibody". www.genecards.org. Retrieved 2015-05-06. CS1 ...
pathway databases. *2D and 3D protein descriptors[26]. General[edit]. *Python wrapper; see Cinfony ... "ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins". BMC ...
Databases: *. Roberts RJ, Vincze T, Posfai, J, Macelis D. "REBASE". Archived from the original on 2016-12-30. Retrieved 2008-06 ... They are used to assist insertion of genes into plasmid vectors during gene cloning and protein production experiments. For ... 35 (Database issue): D269-70. doi:10.1093/nar/gkl891. PMC 1899104. PMID 17202163.. ... RCSB Protein Data Bank. Archived from the original on 2008-05-31. Retrieved 2008-06-06.. ...
Also from GenBank are the protein sequence predictions and annotations. Antimicrobial Resistance databases Wallace, James C.; ... a functional antibiotic resistance element database". Database. 2017: baw165. doi:10.1093/database/baw165. ISSN 1758-0463. PMC ... It is the first database to focus on functional metagenomics. This allows the database to understand 99% of bacteria which ... Antibiotic Resistance Metagenomic Element is a database that compiles publicly available DNA elements and predicted proteins ...
C22orf25 is also xenologous to T10 like proteins in the Fowlpox Virus and Canarypox Virus. The gene coding for C22orf25 is ... "Molecular Interaction Database". Archived from the original on 2006-05-06. CS1 maint: discouraged parameter (link) "Molecular ... Casey PJ (1995). "Protein lipidation in cell signaling". Science. 268 (5208): 221-5. Bibcode:1995Sci...268..221C. doi:10.1126/ ... Transport and golgi organization 2 homolog (TANGO2) also known as chromosome 22 open reading frame 25 (C22orf25) is a protein ...
Universal protein resource accession number GSTZ1 for "Maleylacetoacetate isomerase" at UniProt. Lim CE, Matthaei KI, Blackburn ... "Glutathione". PubChem Compound Database. National Center for Biotechnology Information. U.S. National Library of Medicine. ... "3,5-Dioxooctanedioic acid". PubChem Compound Database. National Center for Biotechnology Information. U.S. National Library of ... Universal protein resource accession number O43708 for "Maleylacetoacetate isomerase" at UniProt. " ...
Integrative neuroscience attempts to consolidate these observations through unified descriptive models and databases of ... proteins, and chemical coupling to network oscillations, columnar and topographic architecture, and learning and memory. ...
endoplasmic reticulum unfolded protein response. · protein localization to nucleus. · sterol regulatory element binding protein ... It stays associated with the membrane through protein-protein interactions of itself and other membrane associated proteins, ... activation of signaling protein activity involved in unfolded protein response. · mitotic nuclear envelope disassembly. · ... protein binding. 细胞成分. · nucleus. · nuclear envelope. · lamin filament. · nuclear lamina. · nucleoplasm. · cytoplasm. · cytosol ...
"Plant Database". School of Horticulture, Kwantlen Polytechnic University. 2015. Retrieved 9 March 2017.. ... The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars than, ... further processed by chemical synthesis into more complex organic molecules such as proteins or cellulose, the basic structural ... chemicals which hinder the digestion of proteins and have an unpleasant taste. Animals that are specialized to eat leaves are ...
"USDA National Nutrient Database, Release 28. 2014. Retrieved 15 May 2013.. *^ Ishida M, Hara M, Fukino N, Kakizaki T, Morimitsu ... 100 grams of raw white cauliflower provides 25 calories, is low in fat, carbohydrates, dietary fiber and protein (table).[20] ...
... protein.[45] PPARα increases the activity of activator protein 1 (AP-1) and NF-κB, thereby leading to the recruitment of ... "The Cochrane Database of Systematic Reviews. 3: CD011154. doi:10.1002/14651858.CD011154.pub2. PMC 7077870. PMID 32175593.. ... "The Cochrane Database of Systematic Reviews. 11: CD009435. doi:10.1002/14651858.cd009435.pub2. PMC 6383843. PMID 30484286.. ... "The Cochrane Database of Systematic Reviews. 9: CD007917. doi:10.1002/14651858.CD007917.pub2. PMC 6457763. PMID 27670126. ...
... online database]. Washington DC: The World Bank; 2015". World Development Indicators [online database]. Retrieved 6 September ... The most common form of malnutrition is protein energy malnutrition (PEM). The other forms of malnutrition are iodine, iron and ... Control of Protein Energy Malnutrition (PEM) c) Control of Iodine Deficiency Disorder (IDD) d) Control of Vitamin A Deficiency ...
GO:0001948 protein binding. • carbohydrate binding. • identical protein binding. • receptor ligand activity. • extracellular ... "EggNOG Database , Orthology predictions and functional annnotaion". eggnogdb.embl.de. Retrieved 5 March 2019.. ... Zona pellucida sperm-binding protein 3, also known as zona pellucida glycoprotein 3 (Zp-3) or the sperm receptor, is a ZP ... The protein encoded by this gene is a major structural component of the ZP and functions in primary binding and stimulation of ...
Inggris) coliBASE: a comparative genomics database for E. coli. *(Inggris) EchoBASE: an integrated post-genomic database for E ... sehingga menghentikan sintesis protein.[1] Sumber bakteri ini contohnya adalah daging yang belum masak, seperti daging ...
"Composition of Foods Raw, Processed, Prepared USDA National Nutrient Database for Standard Reference, Release 26 Documentation ... "Ethanol Causes Acute Inhibition of Carbohydrate, Fat, and Protein Oxidation and Insulin Resistance". J. Clin. Invest. 81 (4): ...
"GM Crop Database: Event 1345-4". International Life Sciences Institute.. *^ Marcia Wood (July 1995). "Bioengineered Tomatoes ... Kurstaki Insect Control Protein". Nature Biotechnology. 7 (12): 1265-1269. doi:10.1038/nbt1289-1265.. ... "Fruit Cell Wall Proteins Help Fungus Turn Tomatoes From Ripe To Rotten". Science Daily. Jan 31, 2008. Retrieved 29 August 2010. ... This tomato gained the moniker "fish tomato".[16] The antifreeze protein was found to inhibit ice recrystallization in the ...
proteins. In enzymology, a beta-alanine-pyruvate transaminase (EC 2.6.1.18) is an enzyme that catalyzes the chemical reaction ... Databases. IntEnz. IntEnz view. BRENDA. BRENDA entry. ExPASy. NiceZyme view. KEGG. KEGG entry. ...
This form of motility has been shown to be regulated by the cAMP receptor protein. Hedger 11:30, 14 2007. The mechanism for ... sorry, but there's no way to confirm 5 year old journal entries, I know for a fact my campus database doesn't even retain ... the nitrogen-fixing protein complex may be packaged into specialized cells called heterocysts." Aren't bacteria single-celled? ... However it is a somewhat ineffective method as it causes the organism to degrade protein, a very metabolically expensive method ...
The B. natans genome contains 293 genes that code for proteins as compared to the 465 genes in G. theta. B. natans also only ... an entry is the submission of a sequence to the DDBJ/EMBL/GenBank public database of sequences). Most sequenced organisms were: ... Most of the genes that moved to the host cell involved protein synthesis, leaving behind a compact genome with mostly single- ... The genome contains 513 genes, 465 of which code for protein. Thirty genes are considered "plastid" genes, coding for plastid ...
Alfa-2 (α2) adrenergički receptor (ili adrenoceptor) je G protein-spregnuti receptor koji vezuje Gi heterotrimerni G protein. ... "IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology. http://www.iuphar-db.org ...
... protein itself is not lost).[16] Lentils have the second-highest ratio of protein per calorie of any legume, after soybeans. ... According to the USDA National Nutrient Database, 100 g of raw lentils (variety unspecified) provide 353 calories; the same ... Raw lentils are 8% water, 63% carbohydrates including 11% dietary fiber, 25% protein, and 1% fat (table). Lentils are a rich ... "Conde Nast, USDA National Nutrient Database, version SR-21. 2014. Retrieved 24 March 2015.. ...
The balance between potassium and sodium is maintained by ion transporter proteins in the cell membrane.[231] The cell membrane ... "The Internet Database of Periodic Tables". meta-synthesis.com. Retrieved 6 April 2012 ...
Human Protein Reference Database (HPRD). *Sequence analysis. *UniProt. *List of sequenced eukaryotic genomes ... The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for ... 41 (Database issue): D36-D42. doi:10.1093/nar/gks1195. PMC 3531190. PMID 23193287.. ... 39 (Database issue): D32-37. doi:10.1093/nar/gkq1079. PMC 3013681. PMID 21071399.. ...
"BRENDA (BRaunschweig ENzyme DAtabase). Helmholtz Centre for Infection Research.. *^ Tranchimand S, Brouant P, Iacazio G (Nov ... Quercetin also activates or inhibits the activities of a number of proteins.[22] For example, quercetin is a non-specific ... "USDA Database for the Flavonoid Content of Selected Foods, Release 3" (PDF). U.S. Department of Agriculture. 2011.. ... quercetin has also been found to act as an agonist of the G protein-coupled estrogen receptor (GPER).[26][27] ...
Mutations in the RPS6KA3 disturb the function of the protein, but it is unclear how a lack of this protein causes the signs and ... The mission of the Foundation is to provide informational links, resources, and databases to families and patients dealing with ... The RPS6KA3 gene makes a protein that is involved with signaling within cells. Researchers believe that this protein helps ... The protein RSK2 which is encoded by the RPS6KA3 gene is a kinase which phosphorylates some substrates like CREB and histone H3 ...
Source: USDA Nutrient Database. Beta carotene, vitamin K, vitamin C, an calcium is rowth in kail. Kail is a soorce o twa ...
The term alpha-1 refers to the protein's behavior on protein electrophoresis. On electrophoresis, the protein component of the ... The MEROPS online database for peptidases and their inhibitors: I04.001 Proteopedia: Alpha-1-antitrypsin Alpha-1 antitrypsin at ... which could confer this protein particular protein-cell recognition properties. The single cysteine residue of A1AT in position ... As protein electrophoresis is imprecise, the A1AT phenotype is analysed by isoelectric focusing (IEF) in the pH range 4.5-5.5, ...
"The Reptile Database". Retrieved February 23, 2016.. *^ Tod W. Reeder, Ted M. Townsend, Daniel G. Mulcahy, Brice P. Noonan, ... The albumin (9) further protects the embryo and serves as a reservoir for water and protein. The allantois (8) is a sac that ... Sri Lanka Wild Life Information Database. *Biology of the Reptilia is an online copy of the full text of a 22 volume 13,000 ... The yolk sac (2) surrounding the yolk (3) contains protein and fat rich nutrients that are absorbed by the embryo via vessels ( ...
2003). "Decline in invasive pneumococcal disease after the introduction of protein-polysaccharide conjugate vaccine". N. Engl. ... Cochrane database of systematic reviews. 1: CD008965. doi:10.1002/14651858.CD008965.pub3. PMID 22258996.. CS1 maint: multiple ... Cochrane database of systematic reviews. 3: CD006607. doi:10.1002/14651858.CD006607.pub4. PMID 22419316.. CS1 maint: multiple ... Cochrane database of systematic reviews. 9: CD004418. doi:10.1002/14651858.CD004418.pub4. PMID 22972070.. CS1 maint: multiple ...
Low-carbohydrate diets such as Atkins and Protein Power are relatively high in protein and fats. Low-carbohydrate diets are ... Cochrane Database of Systematic Reviews. USA (published 18 July 2007). 3 (3): CD005105. doi:10.1002/14651858.CD005105.pub2. ... "Advice on low-fat diets for obesity". Cochrane Database of Systematic Reviews (2): CD003640. doi:10.1002/14651858.CD003640. ... "Low glycaemic index or low glycaemic load diets for overweight and obesity". Cochrane Database of Systematic Reviews (3): ...
Source: USDA Nutrient Database. When cooked, plain pasta is composed of 62% water, 31% carbohydrates (26% starch), 6% protein, ... Gluten, the protein found in grains such as wheat, rye, spelt, and barley, contributes to protein aggregation and firm texture ... Another major component of durum wheat is protein which plays a large role in pasta dough rheology.[53] Gluten proteins, which ... Starch gelatinization and protein coagulation are the major changes that take place when pasta is cooked in boiling water.[53] ...
... it was thought that the sole important retinoid delivery pathway to tissues involved retinol bound to retinol-binding protein ( ... See the USDA Nutrient Database for the amount of Vitamin A http://ndb.nal.usda.gov/ ...
The elimination half-life is around 2 hours.[8][118] It is moderately bound to plasma proteins, especially albumin.[8] However ... Hughes, JR.; Stead, LF.; Lancaster, T. (2007). "Antidepressants for smoking cessation". Cochrane Database Syst Rev (1): ... binding to cAMP-dependent protein kinase (PKA).[111] ...
"PRINTS-a protein motif fingerprint database". Protein Engineering 7 (7). ISSN 1741-0134, Páxs. 841-848.. ... a new generation of protein database search programs". Nucleic Acids Research 25 (17). Págs. 3389-402.. ... "A structural perspective on protein-protein interactions" (PDF). Current Opinion in Structural Biology 14. Páxs. 313-324. ... 2005). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (en inglés) (third edition ed.). Wiley. ISBN 0- ...
proteins. In enzymology, a 2-alkenal reductase (EC 1.3.1.74) is an enzyme that catalyzes the chemical reaction ... Databases. IntEnz. IntEnz view. BRENDA. BRENDA entry. ExPASy. NiceZyme view. KEGG. KEGG entry. ...
Source: USDA Nutrient Database. Basella alba is an edible perennial vine in the family Basellaceae. It is found in tropical ... It is low in calories by volume, but high in protein per calorie. The succulent mucilage is a particularly rich source of ...
... literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein ... Protein-protein interactions Functional associations Protein-protein interaction databases Pathways Protein-protein interaction ... Szklarczyk D., Jensen L.J. (2015) Protein-Protein Interaction Databases. In: Meyerkord C., Fu H. (eds) Protein-Protein ... Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather ...
Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage- ... The current release of Pfam (22.0) contains 9318 protein families. ... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile ... title = {Pfam protein families database},. booktitle = {Nucleic Acids Research, 2008, 36(Database issue): D281-D288},. year ...
Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to ... The database provides spatial arrangement of proteins in the lipid bilayer. Data types. captured. Protein structures from the ... The database was widely used in experimental and theoretical studies of membrane-associated proteins.[13][14][15][16][17] ... ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science ...
The Princeton Protein Orthology Database (P-POD), developed by the Genome Databases Group at Princeton, computes and displays ... Download The Princeton Protein Orthology Database for free. ... The Princeton Protein Orthology Database. Status: Beta. Brought ... Follow The Princeton Protein Orthology Database. The Princeton Protein Orthology Database Web Site ... The Princeton Protein Orthology Database (P-POD), developed by the Genome Databases Group at Princeton, computes and displays ...
... of protein family databases for automatic protein functional classification increases ... As new protein sequences continue to flood into public databases with the advancement of sequencing technologies, the ... Database 10.1093/database/base019. Bru C, Courcelle E, Carrere S et al. (2005) The ProDom database of protein domain families: ... Database 10.1093/database/bar033. Redfern O, Grant A, Maibaum M and Orengo C (2005) Survey of current protein family databases ...
2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17. Research Support, Non-U.S. Govt ... The Pfam protein families database.. Finn RD1, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, ... Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have ... New Pfam display of a protein domain architecture. Pfam-A families classified as type family and domain with a lozenge ...
2014 Jan;42(Database issue):D222-30. doi: 10.1093/nar/gkt1223. Epub 2013 Nov 27. Research Support, Non-U.S. Govt ... Pfam: the protein families database.. Finn RD1, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington ... is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0 ... The results are shown with the protein coordinates of the open reading frame, but it is also possible to toggle this to DNA ...
Dear Yeastnetters, A new database for the proteins of S. cerevisiae has been released from the QUEST Protein Database Center at ... This database, called YPD (Yeast Protein Database), can be downloaded from ftp isis.cshl.org in directory pub/yeast/YPD. The ... The database will be updated periodically to include new yeast proteins that appear in the sequence databases and to add new ... Yeast_Protein_Database. Jim Garrels quest7!jg at ISIS.CSHL.ORG Wed Nov 23 22:54:43 EST 1994 *Previous message: NO SUBJECT ...
15-million grant to combine three of the worlds current protein sequence databases into a single global resource. ... Throwing its financial support behind the concept of a centralized repository for protein data, the National Human Genome ... Dubbed the United Protein Database, or UniProt, the new, public database will combine the resources of three existing protein ... Funding for global protein database. NIH/National Human Genome Research Institute. Funder. National Institutes of Health. ...
The Nuclear Protein Database (NPD) contains information on proteins that are localized to the nuclei of vertebrate cells. Over ... When known, the sub-nuclear compartment where the protein was found is reported. The NPD also provides information on a ... proteins amino acid sequence, predicted size, and isoelectric point, as well as any repeats, motifs, or domains within the ... 1000 vertebrate proteins, mainly from mice and humans, are included. ...
Would ,, anybody be so kind to tell me about: ,, ,, (1). the protein structure databases (PIR, PDB, GenBank...) and their ,, ... Help about protein database.. Cornelius Krasel zxmkr08 at studserv.zdv.uni-tuebingen.de Wed Jun 9 05:05:00 EST 1993 *Previous ... Help about protein database. ,, ,, Hello friends: ,, ,, Im currently a computer science graduate student and going to have a ... Please send any suggestion or answer to: The only 3D database I know of is the protein data bank (PDB). All the others archive ...
... Michael Parker mparker at fhcrc.org Tue Oct 18 20:16:25 EST 1994 *Previous message: Intron ... I need to identify all proteins in swiss_prot, PIR, and genepept which are Saccharomyces and between 12Kdal and 20Kdal. Anyone ...
Pick a protein such as insulin, and the database specifies what proteins, nucleic acids, and other molecules it interacts with ... DNA often gets the glory, but hardworking proteins actually build our bodies and keep them running. Scientists can find out how ... Users can submit their own information to the database, which so far has information on more than 6200 interactions. The site ... You can also learn what biochemical pathways a particular protein participates in and whether it belongs to any larger ...
Features include a general database search, a graphical tool for visualizing the mitochondrial DNA sequences, and 3D structures ... and the Human Mitochondrial Genome Database. HMPDb is intended as a tool not only to aid in studying the mitochondrion but in ... conveniently consolidates information from a number of other databases, including GenBank, Online Mendelian Inheritance in Man ... for mitochondrial proteins. Users are welcome to contact the National Institute of Standards and Technology with corrections or ...
... an orthologous protein, a record from another database, etc.,/p> ,p>,a href="/manual/evidences">More...,/a>,/p> Skip Header ... i ,p>When browsing through different UniProt proteins, you can use the basket to save them, so that you can back to find or ... UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics ...
The information on protein function, as essentialcomponent of biological systems, is essential for the development of biology ... Keywords: protein; database; annotation; text mining; protein function; protein structure; protein domains; posttranslational ... APPRIS, as example of a secondary database based on the information provided by the core protein databases. The APPRIS database ... of the many protein databases, which status is periodically reviewed and maintained in The Molecular Biology Database ...
... able to identify proteins, characterize post-translational modifications, and... ... Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, ... Protein identification MS/MS spectra Protein sequence databases Peptide identification Search engine ... Protein Identification from Tandem Mass Spectra by Database Searching. In: Wu C., Arighi C., Ross K. (eds) Protein ...
... database gives you practical solutions to protect yourself and your family from everyday exposures to chemicals in personal ...
... some products may be missing from the database. If you have purchased a product not currently in the database and have the ... Thus, these reports are solely for your use and will not be made public in the database. ...
Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely ... AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and ... AMYPdb: a database dedicated to amyloid precursor proteins BMC Bioinformatics. 2008 Jun 10;9:273. doi: 10.1186/1471-2105-9-273 ... Results: We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have ...
Protein Databases on the Internet. Dong Xu and Ying Xu. Version of Record online: 1 MAY 2001 , DOI: 10.1002/0471142727. ... Protein Databases on the Internet (pages 19.4.1-19.4.15). Dong Xu and Ying Xu ... Protein Databases on the Internet. Current Protocols in Molecular Biology. 68:19.4:19.4.1-19.4.15. ... Protein Databases on the Internet (pages 19.4.1-19.4.17). Dong Xu ...
The studys authors said they have been overwhelmed by reactions to their finding that curation of protein-protein interaction ... Study Finding Erroneous Protein-Protein Interactions in Curated Databases Stirs Debate. Jan 16, 2009 ... A new study published in Nature Methods that determined that literature-curated protein-protein interaction databases "can be ... Home » Tools & Technology » Informatics » Study Finding Erroneous Protein-Protein Interactions in Curated Databases Stirs ...
N. J. Edwards, "Protein identification from tandem mass spectra by database searching," Methods in Molecular Biology, vol. 694 ... Method for Rapid Protein Identification in a Large Database. Wenli Zhang1,2,3 and Xiaofang Zhao1 ... D. Li, Y. Fu, R. Sun et al., "pFind: a novel database-searching software system for automated peptide and protein ... "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database," Journal of the ...
Protein C in pneumonia. Choi, G., Schultz, M. J., Levi, M., van der Poll, T., Millo, J. L. & Garrard, C. S., Aug-2005, In : ...
... Wenli Zhang1,2,3 and Xiaofang Zhao1 ... Wenli Zhang and Xiaofang Zhao, "Method for Rapid Protein Identification in a Large Database," BioMed Research International, ...
Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. ... In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. ... From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 ... Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of ...
Protein-databases. In this part of the exercise, we shall extract information from the protein-database, Uniprot. This database ... Under "Family and domain databases" you find a long list of databases that using different techniques have collected proteins ... and in some cases can the databases tell which parts of the actual protein that are known in other species.Some large proteins ... Exercise: Translation and protein-databases. Exercise written by: Rasmus Wernersson, Henrik Nielsen and Morten Nielsen ...
Protein Identification - Mass Spectrometry. Databases. ». Applications for Mass Spectrometry. Next Chapter - Protein Primary ... As of 2010, humans are represented the most in the database, covering about 38% of all protein data and 36% of all peptide data ... Proteomics/Protein Identification - Mass Spectrometry/Databases. From Wikibooks, open books for an open world ... These are the Ontology Lookup Service (OLS) and the Protein Identifier Cross-Reference System (PICR). Database on Demand (DoD) ...
... have formed a joint venture to sell a new database of protein and genomic information, the companies said Friday. ... Confirmants database, called the Protein Atlas, will contain information linking the proteins OGS has identified from tissue ... The protein sequence information is compared with genomic data archived in the Ensembl database, a joint project between the ... To build its database, OGS characterizes proteins extracted from cells using 2-D gel electrophoresis and mass spectrometry. ...
... is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in ... Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, ... Human Protein Reference Database--2009 update Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72. doi: 10.1093/nar/gkn892. ... Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic ...
  • Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. (springer.com)
  • Murali T, Pacifico S, Yu J, Guest S et al (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. (springer.com)
  • Proteomics research - the large-scale study of proteins and their interactions - has accelerated in recent years because of technological advances in protein science and the large amounts of genomic data pouring out of the Human Genome Project (HGP). (eurekalert.org)
  • Users can submit their own information to the database, which so far has information on more than 6200 interactions. (sciencemag.org)
  • The information on proteins is organised in databases that store their sequences, domain organisation, three‐dimensional structures, posttranslational modifications, interactions, molecular functions and other protein features. (els.net)
  • RNA-protein interactions play critical roles in various biological processes. (mdpi.com)
  • By collecting and analyzing the RNA-protein interactions and binding sites from experiments and predictions, RNA-protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. (mdpi.com)
  • In short, these RNA-protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA-protein interactions. (mdpi.com)
  • This important tool will help the protein interaction researcher find and display interaction data with ease, using a database with over 190,000 binary interactions from over 10,000 curated experiments. (openhelix.com)
  • Tools that are involved with protein interactions and pathway features. (openhelix.com)
  • For this week's tip of the week I'm going to introduce iRefWeb, a resource that provides thousands of data points on protein-protein interactions. (openhelix.com)
  • PDB Lite derived from OCA, PDB Lite was provided to make it as easy as possible to find and view a macromolecule within the PDB PDBsum provides an overview macromolecular structures in the PDB, giving schematic diagrams of the molecules in each structure and of the interactions between them PDBTM the Protein Data Bank of Transmembrane Proteins - a selection of the PDB. (wikipedia.org)
  • The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. (ncbs.res.in)
  • Core genes/proteins central to the process are assembled with expert input and relevant publications curated for biological interactions. (thebiogrid.org)
  • This is probably because this database contains mainly yeast protein interactions where it is very strong. (openwetware.org)
  • Keating lab]] also works on protein-protein interactions. (openwetware.org)
  • For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity. (mdpi.com)
  • Paul Labute said, "The ability to understand the statistical relevance of protein-ligand or protein-protein interaction motifs using scatter plots, histograms, or sorting by constraint values will allow researchers to make more informed decisions about critical interactions and to facilitate drug design. (chemcomp.com)
  • For more information on peripheral proteins please refer to Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2007) The role of hydrophobic interactions in positioning of peripheral proteins in membranes. (umich.edu)
  • Although protein-peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. (kuleuven.be)
  • A reliable data set of nonredundant protein-peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein-peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. (kuleuven.be)
  • In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. (kuleuven.be)
  • RINGdb contains information on mutations, tissue distributions, protein-protein interactions, diseases/disorders and other features, which has been automatically collected from the Internet and manually extracted from the literature. (biomedcentral.com)
  • Glycine-rich regions are proposed to be involved in protein-protein interactions in some mammalian protein families. (ufrgs.br)
  • The InterPro annotation of families includes short name, name, abstract, GO terms and cross-references to specialized databases and protein s. (psu.edu)
  • Public databases continue to have abnormal, incomplete and mispredicted genes and proteins in spite of the recent efforts made to improve the computational annotation of genomes. (europa.eu)
  • Frequently, several alternative names are in use for biological objects such as genes and proteins. (biomedcentral.com)
  • Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. (biomedcentral.com)
  • Genes and proteins are biological objects of primary importance for understanding biochemical processes. (biomedcentral.com)
  • Public databases aim at organizing information by assigning unique identifiers to genes and proteins. (biomedcentral.com)
  • The human genome project and cDNA project are providing enormous amount of nucleic acid sequences and predicting genes and proteins. (nii.ac.jp)
  • Mann M, Wilm M (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. (springer.com)
  • Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. (springer.com)
  • The database has been constantly growing and in the past two years between 2008 and 2010 it has exploded to contain over two and a half million protein IDs and eleven and a half million peptides. (wikibooks.org)
  • Specific information have been obtained for 10,654 distinct peptides ( Figure 1 ) corresponding to 1,323 validated proteins. (cea.fr)
  • ARTICLE{Eng94anapproach, author = {Jimmy K. Eng and Ashley L. Mccormack and John R. Yates}, title = {An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database}, journal = {J. Am. Soc. (psu.edu)
  • A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. (psu.edu)
  • Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matchmg of the spectra to amino acid sequences within proteins of these organisms. (psu.edu)
  • OPM includes all unique experimental structures of transmembrane proteins and some peripheral proteins and membrane-active peptides ( Features ). (umich.edu)
  • Our calculations are in agreement with experimental studies of 24 transmembrane and 39 peripheral peptides and proteins ( Comparison with Experiments ). (umich.edu)
  • Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database. (kuleuven.be)
  • Protein identification routine as well as posttranslational modification analysis is based on correlation between the mass spectrometry data of peptides obtained from proteome and the entry sequences in the database. (eurekaselect.com)
  • We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware before adopting protein interaction databases in any single-gene or genome-wide analysis. (springer.com)
  • These protein family databases or integrated resources have a number of applications in modern biology or bioinformatics, including protein functional annotation, orthologue prediction, protein-protein interaction prediction, gene set enrichment analysis and providing datasets for evaluation of mathematic models of biological systems or networks. (els.net)
  • As the MisPred routines are able to detect many of these errors, and may aid in their correction, we suggest that it may significantly improve the quality of protein sequence data based on gene predictions. (europa.eu)
  • Find your target protein by entering the protein name, gene symbol or accession number in the search box below. (genscript.com)
  • Test the protective effect of the coat protein of satellite panicum mosaic virus on the stability of plant virus-derived gene expression vectors. (epa.gov)
  • Also, includes protein pathways and gene sequences including other tools. (wikipedia.org)
  • Use our database to quickly find validated sequence information for full-length gene sequences and open reading frame (ORF) sequences for your gene of interest. (genscript.com)
  • Several mutations of the gene are associated with phenotypic functional deficiency of protein C, and with the risk of developing venous thrombosis. (cnr.it)
  • It is an excellent resource for students and professionals involved with gene or protein expression data in a variety of settings. (wiley.com)
  • Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. (biomedcentral.com)
  • These databases can be used for deriving gene and protein name dictionaries. (biomedcentral.com)
  • We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. (biomedcentral.com)
  • We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. (biomedcentral.com)
  • In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. (biomedcentral.com)
  • Besides sequences, biochemical properties, and other information, these databases also contain gene and protein names. (biomedcentral.com)
  • The latter contains high-quality annotations, yet the protein names are contained in different database fields: the "Gene name" field, which is easy to parse automatically and the description field, that contains long forms, and is more difficult to parse due to nested parentheses which sometimes represent separate synonyms of varying specificity and sometimes are subtypes, specifications of or additions to previous synonyms (e.g. (biomedcentral.com)
  • These proteins should be demonstrated to be real gene products and characterizad with their forms in the cells. (nii.ac.jp)
  • Orientations of Proteins in Membranes ( OPM ) database provides spatial positions of membrane protein structures with respect to the lipid bilayer . (wikipedia.org)
  • Proteins structures are taken from the Protein Data Bank . (wikipedia.org)
  • The site allows visualization of protein structures with membrane boundary planes through Jmol . (wikipedia.org)
  • This is the case when all membrane-anchoring parts of the proteins ( amphiphilic alpha helices , exposed nonpolar residues, or lipidated amino acid residues ) are missing in the experimental structures. (wikipedia.org)
  • [4] The database also does not include lower resolution structures with only main chain atoms provided by the Protein Data Bank . (wikipedia.org)
  • The calculated spatial arrangements of the lower resolution protein structures in the lipid bilayer can be found in other resources, such as PDBTM. (wikipedia.org)
  • You cannot do molecular modelling with it, but it is very nice for viewing protein structures. (bio.net)
  • Features include a general database search, a graphical tool for visualizing the mitochondrial DNA sequences, and 3D structures for mitochondrial proteins. (curriki.org)
  • CExonic and CORSAIR determine patterns of conservation of exonic structures using different type of alignment strategies, similar to the one provided by databases on orthologs and interspecies alignments (see http://questfororthologs.org/orthology_databases ). (els.net)
  • Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. (nih.gov)
  • The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. (nih.gov)
  • In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. (wikipedia.org)
  • The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. (wikipedia.org)
  • Data included in protein structure databases often includes three-dimensional coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. (wikipedia.org)
  • Database of Macromolecular Movements describes the motions that occur in proteins and other macromolecules, particularly using movies Dynameomics a data warehouse of molecular dynamics simulations and analyses of proteins representing all known protein fold families JenaLib the Jena Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. (wikipedia.org)
  • OPM provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer. (wikipedia.org)
  • PDBWiki a community annotated knowledge base of biological molecular structures [1] ProtCID The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins. (wikipedia.org)
  • SWISS-MODEL Repository a database of annotated protein models calculated by homology modeling TOPSAN the Open Protein Structure Annotation Network - a wiki designed to collect, share and distribute information about protein three-dimensional structures. (wikipedia.org)
  • Protein domain superfamilies in CATH-Gene3D have been subclassified into functional families (or FunFams), which are groups of protein sequences and structures with a high probability of sharing the same function(s). (cathdb.info)
  • The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. (ncbs.res.in)
  • If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. (csic.es)
  • My contribution is the LoopWeaver protocol, a database method that uses multidimensional scaling to rapidly achieve better clash-free, low energy placement of loops obtained from a database of protein structures. (uwaterloo.ca)
  • Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. (biomedcentral.com)
  • To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. (biomedcentral.com)
  • Thus, information on both many and few protein structures can be used efficiently. (biomedcentral.com)
  • This trend can also be seen in the field of structural biology, where the number of protein structures deposited in the Protein Data Bank, PDB [ 1 ] is increasing rapidly. (biomedcentral.com)
  • Oberg and colleagues [ 2 ] compared the results from infrared and circular dichroism spectroscopy with the actual 3D structure of a protein to gain insight into the relationship between assigned protein secondary structures and spectral band shape. (biomedcentral.com)
  • In both examples, the first step in the experiments was the compilation of a set of protein structures based on the structure itself and on folding classification, sequence properties, enzymatic activity, and other types of information. (biomedcentral.com)
  • Researchers have several possibilities to collect information on protein structures. (biomedcentral.com)
  • We have built a Protein-Protein Interface Database (PPIDB) which extracted 71, 486 protein-protein interfaces from experimentally determined protein complex structures in the current version of Protein Data Bank. (iastate.edu)
  • Modeled protein structures are generated via homologue modeling and fed as inputs into NB PPIPS. (iastate.edu)
  • Protein structures have been determined and deposited into Protein Data Bank at an increasing rate. (iastate.edu)
  • In this work, we organize all the protein structures in the PDB and form a wild type and mutant structure database. (iastate.edu)
  • The database groups the wild type and mutant structures of the same protein together. (iastate.edu)
  • What distinguishes our work from other mutation databases is that it is structure-based and includes all the existing structures of the PDB. (iastate.edu)
  • A key question we address in this work is: is it valid to use mutant structures (or variants from different species) to represent a native state sample of a given protein? (iastate.edu)
  • This implies that cautions must be taken when mutation structures are considered to be included as representative samples of the conformation space of a given protein. (iastate.edu)
  • Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. (unl.edu)
  • [5] [6] The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes. (wikipedia.org)
  • MPtopo is a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. (vifabio.de)
  • Cherry JM, Hong EL, Amundsen C, Balakrishnan R et al (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. (springer.com)
  • The YPD database was built to assist us in our project to identify and characterize the proteins of budding yeast on 2D gels. (bio.net)
  • Using a combinatorial approach of yeast synthetic genetic array technology, high-content screening, and machine learning classifiers, we developed an automated platform to characterize protein localization and abundance patterns from images of log phase cells from the open-reading frame−green fluorescent protein collection in the budding yeast, Saccharomyces cerevisiae . (g3journal.org)
  • Proteomic analysis using 'spectral count' shows that the first steps (methylerythritol phosphate pathways, the shikimate or protoporphyrinogen IX, for example) take place in the stroma (the proteins are indicated by orange circles) and then, as soon as molecules become hydrophobic, metabolic pathways involve membrane proteins: either from the thylakoids (green circles) or the envelope (yellow circles). (cea.fr)
  • OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer. (umich.edu)
  • Established in 1986 by Amos Bairoch, Ph.D., now a group leader of SWISS-PROT at the Swiss Institute of Bioinformatics (SIB) in Geneva, SWISS-PROT's hands-on, high-quality information processes could not cope with the rising tide of new information coming out of high-throughput DNA sequencing, which has generated information about hundreds of thousands of new proteins from all species being studied, including human. (eurekalert.org)
  • Instead of offering a mere catalogue of the many protein databases, which status is periodically reviewed and maintained in 'The Molecular Biology Database Collection' (http://www.oxfordjournals.org/nar/database/c/), this article reviews the operations necessary to organise and make openly accessible their information as part of the complex ecosystems of bioinformatics infrastructures. (els.net)
  • Bioinformatics infrastructure is the collection of databases, bioinformatics methods, and computational resources that provide the essential support to the work of biologists. (els.net)
  • pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry," Bioinformatics , vol. 21, no. 13, pp. 3049-3050, 2005. (hindawi.com)
  • Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semiquantitative measurements of relative protein abundance. (springer.com)
  • A new study published in Nature Methods that determined that literature-curated protein-protein interaction databases "can be error-prone and possibly of lower quality than commonly assumed" has touched a nerve among proteomics researchers. (genomeweb.com)
  • DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data," Molecular and Cellular Proteomics , vol. 10, no. 5, 2011. (hindawi.com)
  • This article seeks to highlight the recent advances and modifications in the Proteomics Identifications Database and to point out the vital role it plays in the collection and storage of mass spectrometry (MS) data. (wikibooks.org)
  • A database that is centralized, public, and standards compliant and contains a variety of proteomics data. (wikibooks.org)
  • A tool used to view spectra from within the Proteomics Identifications Database. (wikibooks.org)
  • In proteomics, peptide information within mass spectrometry (MS) data from a specific organism sample is routinely matched against a protein sequence database that best represent such organism. (frontiersin.org)
  • Features that are relevant for probabilistic-based protein identification by proteomics were then monitored. (frontiersin.org)
  • Consequently, for any given strain or species, its predicted protein sequence information will normally contain inaccuracies that will interfere with peptide identification in mass spectrometry (MS)-based proteomics. (frontiersin.org)
  • To support this, we established a comprehensive database for synaptic junction proteins (SynProt database) primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. (frontiersin.org)
  • Here, we report the Dynamic Proteomics database for the proteins studied by Cohen et al. (caltech.edu)
  • The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition. (caltech.edu)
  • Amino acid sequence database is one of the essential components in the current proteomics with mass spectrometry. (eurekaselect.com)
  • Takao Kawakami, Junko Ozaki, Kazuhiro Kondo, Shinji Sato and Harunobu Yunokawa, " Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis", Current Proteomics (2008) 5: 267. (eurekaselect.com)
  • Dubbed the United Protein Database, or UniProt, the new, public database will combine the resources of three existing protein databases: SWISS-PROT, TrEMBL and the Protein Information Resource (PIR). (eurekalert.org)
  • These advances have strained the ability of one protein database - SWISS-PROT, a hand-curated and annotated protein-sequence database - to keep pace with the needs of the world's scientists. (eurekalert.org)
  • TrEMBL was developed to handle the increasing amounts of data being generated by large-scale genomic projects, allowing scientists quicker access to new protein sequences before they were hand-curated and entered into SWISS-PROT. (eurekalert.org)
  • To achieve this vision of a centralized protein database, NHGRI decided to fund the UniProt project, which will consolidate and build upon the strengths of SWISS-PROT and TrEMBL, as well as the U.S.-operated database, Protein Information Resource. (eurekalert.org)
  • Specifically, the new UniProt database will consist of two parts: the SWISS-PROT section, which will contain fully annotated entries, and the TrEMBL section, which will contain those computer-annotated records that are waiting hands-on analysis. (eurekalert.org)
  • The PIR group will no longer maintain its database, but will assist in elevating the annotation of TrEMBL records to the SWISS-PROT standard. (eurekalert.org)
  • Nevertheless, the fact that MisPred analyses of protein sequences of the Swiss-Prot database identified very few such exceptions indicates that the rules of MisPred are generally valid. (europa.eu)
  • Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON predicted entries,' the team said. (europa.eu)
  • GenScript maintains a user-friendly interface for searching or browsing UniProtKB/Swiss-Prot and RefSeq validated protein sequences from 185 unique species. (genscript.com)
  • It facilitates construction of well-characterized datasets of protein-protein interface residues for computational analyses. (iastate.edu)
  • In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. (kuleuven.be)
  • Croft D, O'Kelly G, Wu G, Haw R et al (2011) Reactome: a database of reactions, pathways and biological processes. (springer.com)
  • The information on protein function, as essential component of biological systems, is essential for the development of biology and biomedicine. (els.net)
  • Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. (nature.com)
  • SAN FRANCISCO, Dec. 10 - Biological database developer Cognia has received a grant from the National Science Foundation to create a database on protein localization, the company said on Monday. (genomeweb.com)
  • To the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community. (ncbs.res.in)
  • Currently, besides the protein sequences for known human proteins, there are partial sequences from thousands more human proteins for which no biological function has been assigned. (nih.gov)
  • Biological databases have become a major resource for researchers in life science. (biomedcentral.com)
  • Protein-protein interaction plays a pivotal role in biological metabolism. (iastate.edu)
  • To facilitate clinical and pharmacological research, we have developed a novel integrated biological database called RINGdb to provide comprehensive and organized RGS protein and GPCR information. (biomedcentral.com)
  • In alteration of the unmodified precursor sequences according to their biological processes and variations, the altered sequence database allows to output the search results on the matured polypeptides. (eurekaselect.com)
  • Changes in protein subcellular localization and abundance are central to biological regulation in eukaryotic cells. (g3journal.org)
  • Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. (springer.com)
  • Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein. (wikipedia.org)
  • ProCMD is an up-to-date interactive mutant database that integrates phenotypical descriptions with functional and structural data obtained by computational approaches. (cnr.it)
  • We show that by using an approach where database size is controlled by removing repeated identical tryptic sequences across strains/species, computational time can be reduced drastically as database complexity increases. (frontiersin.org)
  • Experimental methods to identify protein-protein interaction sites are always time-consuming and costly, which calls for computational methods to be applied in this area. (iastate.edu)
  • For an explanation of our method please refer to Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2006) Positioning of proteins in membranes: A computational approach. (umich.edu)
  • 3 ) to predict the specificity and relative binding energy of RNA-binding proteins, computational models describing the binding specificity of RBPs (by contrast, for instance, with transcription factors) are lacking ( 4 ). (pubmedcentralcanada.ca)
  • To simplify access to multiple databases by the user, many of these databases have also been amalgamated into integrated protein family resources, which vary in their level of manual curation. (els.net)
  • Process of adding information to database entries by groups of experts typically associated to large databases is known as database curation. (els.net)
  • The BioGRID Open Respository of CRISPR Screens (ORCS) is a publicly accessible database of CRISPR screens compiled through comprehensive curation efforts. (thebiogrid.org)
  • New curated data are added to our CRISPR Database in curation updates on a regular basis. (thebiogrid.org)
  • These databases are quite diverse in terms of organism-specificity, structure, and applied curation procedure. (biomedcentral.com)
  • This combination provides the cancer biologist with the ability to (i) identify the potential protein:protein associations and (ii) fully characterize function-critical post-translational modifications, both directly from silver-stained polyacrylamide gels. (nih.gov)
  • YPD provides a non-redundant list of the known yeast proteins and many of their properties in a spreadsheet format. (bio.net)
  • The database will be updated periodically to include new yeast proteins that appear in the sequence databases and to add new information about the yeast proteins obtained from scans of the current and prior literature. (bio.net)
  • The search currently works only for yeast proteins. (sciencemag.org)
  • This manuscript describes the concepts, prerequisites, and methods required to analyze a tandem mass spectrometry dataset in order to identify its proteins, by using a tandem mass spectrometry search engine to search protein sequence databases. (springer.com)
  • BioGRID update 4.2.191 includes a comprehensive update to our Drosophila melanogaster (Fruit Fly) dataset in collaboration with FlyBase - The Database of Drosophila Genes and Genomes . (thebiogrid.org)
  • If you have a CRISPR Screen Dataset you'd like to deposit directly into the BioGRID ORCS CRISPR Database, please contact us at [email protected] . (thebiogrid.org)
  • Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed). (frontiersin.org)
  • Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. (nih.gov)
  • ModBase a database of three-dimensional protein models calculated by comparative modeling OCA a browser-database for protein structure/function - The OCA integrates information from KEGG, OMIM, PDBselect, Pfam, PubMed, SCOP, SwissProt, and others. (wikipedia.org)
  • The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. (csic.es)
  • RINGdb also integrates organized database cross-references to allow users direct access to detailed information. (biomedcentral.com)
  • 2011) CDD: a conserved domain database for the functional annotation of proteins. (els.net)
  • In this study, a main effort was specifically made for the annotation of proteins from the chloroplast envelope, the site of interaction between plastids and the rest of the cell. (cea.fr)
  • ProtBank™ is an integrated protein database that provides comprehensive, freely accessible information about a protein's sequence, structure, functions, domains, post translational modifications, sub-cellular localization and protein-protein interaction. (genscript.com)
  • The regulation of protein function through reversible phosphorylation by protein kinases and phosphatases is a general mechanism controlling virtually every cellular activity. (pubmedcentralcanada.ca)
  • Eukaryotic protein kinases can be classified into distinct, well-characterized groups based on amino acid sequence similarity and function. (pubmedcentralcanada.ca)
  • We recently reported a highly sensitive and accurate hidden Markov model-based method for the automatic detection and classification of protein kinases into these specific groups. (pubmedcentralcanada.ca)
  • The regulation of protein function through reversible phosphorylation by protein kinases and phosphatases is a widespread cellular mechanism thought to control virtually every cellular activity ( 1 ), and abnormal levels of phosphorylation are known to be responsible for severe diseases ( 2 ). (pubmedcentralcanada.ca)
  • The aPKs are a small set of protein kinases that do not share clear sequence similarity with ePKs, but have been shown experimentally to have protein kinase activity. (pubmedcentralcanada.ca)
  • Protein kinases catalyze the formation of a covalent bond between a phosphate group and a hydroxyl moiety of an amino-acid side chain. (biomedcentral.com)
  • This strategy implemented for the first time has allowed identifying the of subplastidial localization of identified proteins to build the AT_Chloro dabase. (cea.fr)
  • The blue circles correspond to proteins whose localization was not possible. (cea.fr)
  • The database currently contains 2,788 non-redundant entries of rat, mouse, and some human proteins, which mainly have been manually extracted from 12 proteomic studies and annotated for synaptic subcellular localization. (frontiersin.org)
  • The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. (pubmedcentralcanada.ca)
  • For each protein, we produced quantitative profiles of localization scores for 16 subcellular compartments at single-cell resolution to trace proteome-wide relocalization in conditions over time. (g3journal.org)
  • The images depict the localization and abundance dynamics of more than 4000 proteins under two chemical treatments and in a selected mutant background. (g3journal.org)
  • Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage-nomics projects. (psu.edu)
  • TypeError: Cannot read property 'Run' of undefined at Object.proteinURL [as protein] (/usr/local/lib/node_modules/bionode-ncbi/lib/bionode-ncbi.js:431:26) at DestroyableTransform.transform [as _transform] (/usr/local/lib/node_modules/bionode-ncbi/lib/bionode-ncbi.js:410:17) at DestroyableTransform.Transform. (github.com)
  • The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format. (nih.gov)
  • No BLAST database contains all the sequences at NCBI. (nih.gov)
  • recent references: [http://www.ncbi.nlm.nih.gov/pubmed/21071413 The BioGRID Interaction Database: 2011 update], [http://www.ncbi.nlm.nih.gov/pubmed/20489023 A global protein kinase and phosphatase interaction network in yeast. (openwetware.org)
  • Background: A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. (unl.edu)
  • 1997) Gapped BLAST and PSI‐BLAST: a new generation of protein database search programs. (els.net)
  • The site also features PreBIND, a prototype search engine that scans PubMed for articles that mention proteins likely to interact with your chosen molecule. (sciencemag.org)
  • Search your protein of interest to learn more. (genscript.com)
  • The search will be restricted to the sequences in the database that correspond to your subset. (nih.gov)
  • You can use Entrez query syntax to search a subset of the selected BLAST database. (nih.gov)
  • Learn to use the IntAct resource, a protein interaction database with valuable tools that can be used to search for, analyze and graphically display protein interaction data from a wide variety of species. (openhelix.com)
  • To investigate putative conserved sites for your protein sequence, run a sequence search against the FunFams and click on the FunFam match Alignment page. (cathdb.info)
  • We have built a specialized relational database and a search tool for natural mutants of protein C. It contains 195 entries that include 182 missense and 13 stop mutations. (cnr.it)
  • Current web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. (harvard.edu)
  • Chemical Computing Group (CCG) today announces a new version of its structure database and visualization system, PSILO , featuring new analytical tools and enhanced search capabilities. (chemcomp.com)
  • The database can be searched using either keyword search or data source-specific web forms. (biomedcentral.com)
  • Annotations may be incomplete or inconsistent with standard nomenclature, spelling errors and uncontrolled usage of abbreviations prevent an efficient textual search, and literature references or links to functional and structural databases may be outdated or missing. (biomedcentral.com)
  • Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. (unl.edu)
  • While different sequence databases are available from public resources for the correlation search, these primary sequence data can be processed into more useful forms. (eurekaselect.com)
  • Protein the NIH protein database, a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and Third Party Annotation, as well as records from SwissProt, PIR, PRF, and PDB Proteopedia the collaborative, 3D encyclopedia of proteins and other molecules. (wikipedia.org)
  • It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of October 2018). (ncbs.res.in)
  • OPM also provides structural classification of membrane-associated proteins into families and superfamilies, membrane topology , quaternary structure of proteins in membrane-bound state, and the type of a destination membrane for each protein. (wikipedia.org)
  • The APPRIS database contains information on human splice isoforms annotating them with protein structural and functional and evolutionary features. (els.net)
  • Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. (wikipedia.org)
  • SCOP the Structural Classification of Proteins [2] a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. (wikipedia.org)
  • The following instructions demonstrate how to find significant CATH structural domain matches on your own protein sequence. (cathdb.info)
  • Other types of information, such as functional and structural annotations of proteins, also have to be taken into account. (biomedcentral.com)
  • Trained over a non-redundant data set consisting of 2, 383 proteins and fed with sequence, evolutionary and structural properties, NB PPIPS achieves 60.7% recall and 34.6% precision in 10 fold cross-validation, which greatly improves over the baseline classifier that only utilizes protein sequence information. (iastate.edu)
  • In this paper, the structural and functional features of these proteins in Eucalyptus are summarized. (ufrgs.br)
  • ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. (eurekamag.com)
  • Protein family data has a number of applications, notably for the functional classification of new protein sequences. (els.net)
  • The file YPD.doc provides a more complete description of the database and its data fields. (bio.net)
  • YPD currently contains data on 3050 proteins of known sequence. (bio.net)
  • BETHESDA, Md., Oct. 23, 2002 - Throwing its financial support behind the concept of a centralized repository for protein data, the National Human Genome Research Institute (NHGRI), in cooperation with five other institutes and centers at the National Institutes of Health (NIH), has awarded a three-year, $15-million grant to combine three of the world's current protein sequence databases into a single global resource. (eurekalert.org)
  • The only 3D database I know of is the protein data bank (PDB). (bio.net)
  • Perkins DN, Pappin DJ, Creasy DM et al (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. (springer.com)
  • However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases. (nih.gov)
  • We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. (nih.gov)
  • A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. (nih.gov)
  • AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. (nih.gov)
  • Mass Spectrometry databases are a unique challenge for maintaining the vast quantity of data generated from an MS experiment due to both size and complexity issues. (wikibooks.org)
  • Although significant progress has been made in the standardization of these data types, there is still significant incongruence from one spectral database to another. (wikibooks.org)
  • Begun in 1970, the NIST standard reference database is a verbose collection of spectral data in a common data type, requiring both a minimal amount of data regarding the experiment as well as a standard format for the presentation of spectral data from a wide variety of MS applications. (wikibooks.org)
  • One such example of this database type is the Mass Spectrometry Database Committee's comprehensive drug library [3] , which contains spectral data for pharmaceutical substances, metabolites, and intermediate compounds. (wikibooks.org)
  • The data found in the database comes from a vast range of experiments and is stored in a format that allows for simple and complex querying in a common format. (wikibooks.org)
  • The data contained within is primarily protein and peptide IDs, MS mass spectra, and any related metadata. (wikibooks.org)
  • Data base analysis of protein expression patterns during T-cell ontogeny and activation. (pnas.org)
  • We have developed a data base of lymphoid proteins detectable by two-dimensional polyacrylamide gel electrophoresis. (pnas.org)
  • Using this data base, we have compared the protein constituents of mature T cells and immature thymocytes before and after mitotic stimulation. (pnas.org)
  • Since then, six other member databases have also joined and their data has bee. (psu.edu)
  • IntAct captures protein interaction data from peer-reviewed literature and direct user submissions. (openhelix.com)
  • Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. (openhelix.com)
  • These data were then structured in AT_Chloro, a database specific of the chloroplast from Arabidopsis thaliana . (cea.fr)
  • The Protein Data Bank (PDB) was established in 1971 as the central archive of all experimentally determined protein structure data. (wikipedia.org)
  • Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank (wwPDB). (wikipedia.org)
  • Because the PDB releases data into the public domain, the data has been used in various other protein structure databases. (wikipedia.org)
  • The Protein Data Bank: a historical perspective" (PDF). (wikipedia.org)
  • CATH-Gene3D provides information on the evolutionary relationships of protein domains through sequence, structure and functional annotation data. (cathdb.info)
  • We further tested database performance by using MS data from eight clinical strains from M. tuberculosis , and from two published datasets from Staphylococcus aureus . (frontiersin.org)
  • In such cases when the establishment of a gold-standard annotation that can represent the sample under investigation is difficult, a viable alternative is to construct customized protein sequence databases which are then inspected against peptide sequence data collected by MS ( Nesvizhskii, 2014 ). (frontiersin.org)
  • The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins. (harvard.edu)
  • This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive PBM data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. (harvard.edu)
  • In total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse and human. (harvard.edu)
  • Modeling loops is an often necessary step in protein structure and function determination, even with experimental X-ray and NMR data. (uwaterloo.ca)
  • Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. (biomedcentral.com)
  • The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. (biomedcentral.com)
  • The final data set contains 505 unique protein-peptide interface clusters from 1431 complexes. (kuleuven.be)
  • Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. (pubmedcentralcanada.ca)
  • Despite the progress made during the past few decades, our knowledge about regulation of protein function by phosphorylation and the basis of kinase specificity remains incomplete, mainly because of lack of data. (biomedcentral.com)
  • The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. (eurekamag.com)
  • The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. (eurekamag.com)
  • The Princeton Protein Orthology Database (P-POD), developed by the Genome Databases Group at Princeton, computes and displays families of orthologs between multiple organisms. (sourceforge.net)
  • Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. (nature.com)
  • These additions bring our total number of curated CRISPR screens in our database to 1,201 encompassing 64,173+ genes, 698 different cell lines, 114 different cell types, and 18 different phenotypes across 3 different organisms (Human, Mouse, and Fruit Fly). (thebiogrid.org)
  • The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. (biomedcentral.com)
  • The results are shown with the 'protein' coordinates of the open reading frame, but it is also possible to toggle this to DNA sequence coordinates. (nih.gov)
  • 2012) Gene3D: a domain‐based resource for comparative genomics, functional annotation and protein network analysis. (els.net)
  • Functional annotation is a process of assigning function to a protein based on the experimental evidence published in the literature or transferred from other proteins with similar sequences. (els.net)
  • CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. (unl.edu)
  • Nucleic Acids Research 36(Database issue): D419-D425. (els.net)
  • Nucleic Acids Research 39(Database issue): D420-D426. (els.net)
  • Nucleic Acids Research 38(Database issue): D211-D222. (els.net)
  • Nucleic Acids Research 38(Database issue): D331-D335. (els.net)
  • Nucleic Acids Research 40(Database issue): D465-D471. (els.net)
  • Nucleic Acids Research 39(Database Issue): D225-D229. (els.net)
  • Nucleic Acids Research 33(Database issue): D226-D229. (els.net)
  • Nucleic Acids Research 41(Database issue): D110-D117. (els.net)
  • Fernández‐Suárez XM, Rigden DJ and Galperin MY (2014) The 2014 nucleic acids research database issue and an updated NAR online molecular biology database collection. (els.net)
  • Nucleic Acids Research 42(Database issue): D1-D6. (els.net)
  • Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. (psu.edu)
  • The current release of Pfam (22.0) contains 9318 protein families. (psu.edu)
  • Pfam is a widely used database of protein families and domains. (nih.gov)
  • New Pfam display of a protein domain architecture. (nih.gov)
  • Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. (nih.gov)
  • Pfam-B entries are automatically generated from the ProDom database =-=(3)-=-, and are represented by a single alignment. (psu.edu)
  • INTRODUCTION InterPro (1) is an integrative database which was founded 10 years ago when the PROSITE (2), PRINTS (3), Pfam (4) and ProDom =-=(5)-=- databases formed a consortium to amalgamate the predictive signatures they individually produced into a single resource. (psu.edu)
  • The Kinomer v. 1.0 database presented here contains annotated classifications for the protein kinase complements of 43 eukaryotic genomes. (pubmedcentralcanada.ca)
  • The post-genomic era is characterized by the deposition of sequence information for entire genomes in databases. (nih.gov)
  • Portugaly E, Linial N and Linial M (2007) EVEREST: a collection of evolutionary conserved protein domains. (els.net)
  • The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). (csic.es)
  • Sadygov RG, Cociorva D, Yates JR (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. (springer.com)
  • Craig R, Beavis RC (2004) Tandem: matching proteins with tandem mass spectra. (springer.com)
  • It is therefore crucial to identify which proteins can be modified as well as the effect and lifetime of the PTMs. (biomedcentral.com)
  • The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download. (ncbs.res.in)
  • The first is the identification of gel-separated, low abundance proteins based on amino acid sequence composition following coimmunoprecipitation with the human apoptosis inhibitor protein BclX(L). The second is the determination of the precise sites of phosphorylation of the human regulatory protein 4E-BP1, which controls mRNA translation. (nih.gov)
  • The creation of this database will allow performing further analyses by nanoLC-FT-MS, avoiding the systematic use of MS / MS, thus significantly increasing the speed of analysis and coverage of the studied proteome. (cea.fr)
  • Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. (nih.gov)
  • The UniProt database will become a resource for all scientists to use, both to develop a better understanding of biology and to translate that basic science into clinical applications. (eurekalert.org)
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • Dinkel H, Chica C, Via A, Gould CM et al (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. (springer.com)
  • In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens , M. musculus , R. norvegicus , D. melanogaster , C. elegans , S. pombe and S. cerevisiae . (nature.com)
  • From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. (nature.com)
  • Information transfer is a process of assigning functions or functional characteristics to protein sequences based on the annotations of similar - in most cases orthologos - sequences. (els.net)
  • Combining annotations from different publications and database to produce a representative description of protein characteristics and functional properties is known as information integration. (els.net)
  • The following instructions demonstrate how to find function annotations for your own protein sequence. (cathdb.info)
  • Caspi R, Foerster H, Fulcher CA, Kaipa P et al (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. (springer.com)
  • You can also learn what biochemical pathways a particular protein participates in and whether it belongs to any larger conglomerations of molecules. (sciencemag.org)
  • Quantitative measures of protein dynamics in vivo are therefore highly useful for elucidating specific regulatory pathways. (g3journal.org)
  • GenScript maintains the GenPool™ ORF clones database, the world's largest commercial ORF clone database with over 2,428,863 ORF clones from 186 different species. (genscript.com)
  • However, if the species/strain in the sample is unknown or genetically poorly characterized, it becomes challenging to determine a database which can represent such sample. (frontiersin.org)
  • Building customized protein sequence databases merging multiple strains for a given species has become a strategy to overcome such restrictions. (frontiersin.org)
  • To test this assumption, we constructed databases containing conserved and unique sequences for 10 different species. (frontiersin.org)
  • The kinomes are stored in a relational database and are accessible through a web interface on the basis of species, kinase group or a combination of both. (pubmedcentralcanada.ca)
  • The Kinomer v. 1.0 database is a continually updated resource where direct comparison of kinase sequences across kinase groups and across species can give insights into kinase function and evolution. (pubmedcentralcanada.ca)
  • Taylor A, Johnson RS (1997) Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. (springer.com)
  • pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry," Rapid Communications in Mass Spectrometry , vol. 21, no. 18, pp. 2985-2991, 2007. (hindawi.com)
  • A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. (psu.edu)
  • In this report we describe the application of tandem mass spectrometry and database searching to two problems which are prototypical for cancer research and indeed for biomedical research in general. (nih.gov)
  • In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of * 1 u of the precursor ion molecular weight. (psu.edu)
  • We are trying to isolate proteins in the human cells by high resolution two dimensional electrophoresis and provide their amino acid sequences. (nii.ac.jp)
  • Dear Yeastnetters, A new database for the proteins of S. cerevisiae has been released from the QUEST Protein Database Center at the Cold Spring Harbor Laboratory. (bio.net)
  • We have made a comprehensive analysis of protein-protein dimeric interfaces, which consists of thirteen physic-chemical properties. (iastate.edu)
  • Attempts are made to apply the NB PPIPS in a two stage prediction of protein-protein interfaces when only protein sequence is known. (iastate.edu)
  • Goel R, Harsha HC, Pandey A, Prasad TSK (2012) Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. (springer.com)
  • 2012) The PRINTS database: a fine‐grained protein sequence annotation and analysis resource - its status in 2012. (els.net)
  • Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. (nih.gov)
  • In this regard, the identification and functional analysis of phosphosites are fundamental for understanding the molecular mechanisms and regulatory roles of protein phosphorylation. (nature.com)
  • The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). (or.jp)
  • Automatic Quote will be generated only if sequences qualify for the Guaranteed service, as determined by our proprietary sequence analysis platform, failing which, our Technical Account Manager will contact you with a custom protein production quote. (genscript.com)
  • As an application, we carry out an experimental structure-based statistical analysis of the effects of mutations, on both protein structure and protein dynamics. (iastate.edu)
  • To address this need, we have developed the CLIPZ database and analysis environment. (pubmedcentralcanada.ca)
  • The protein dynamics in the database represents a quantitative trace of the protein fluorescence levels in nucleus and cytoplasm produced by image analysis of movies over time. (caltech.edu)
  • Modification of the composition in sequence database would be practically beneficial to the wide range from the detail analysis focusing on a single protein to the biomarker discovery studies for the clinical utility. (eurekaselect.com)
  • The database was widely used in experimental and theoretical studies of membrane-associated proteins. (wikipedia.org)
  • We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design. (frontiersin.org)
  • Hanks and Hunter were the first to report that sequence similarity of kinase catalytic domains reflects protein kinase function and/or mode of regulation ( 3 , 4 ). (pubmedcentralcanada.ca)
  • The currently accepted classification of the eukaryotic protein kinase superfamily considers eight 'conventional' protein kinase groups (ePKs) and four 'atypical' groups (aPKs) ( 5 , 6 ). (pubmedcentralcanada.ca)