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. ...
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 ...
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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: ...
CP000675.HUTI Location/Qualifiers FT CDS 884792..886003 FT /codon_start=1 FT /transl_table=11 FT /gene=hutI FT /locus_tag=LPC_2582 FT /product=imidazolonepropionase FT /db_xref=EnsemblGenomes-Gn:LPC_2582 FT /db_xref=EnsemblGenomes-Tr:ABQ56497 FT /db_xref=GOA:A5IGJ7 FT /db_xref=InterPro:IPR005920 FT /db_xref=InterPro:IPR006680 FT /db_xref=InterPro:IPR011059 FT /db_xref=InterPro:IPR032466 FT /db_xref=UniProtKB/Swiss-Prot:A5IGJ7 FT /protein_id=ABQ56497.1 FT /translation=MFACDELLLNASTIDATGLQLSNQAIVIKKGRIEWCGSEDQLPAH FT FQESAKSRKDCHGQLITPGLIDCHTHLVYAGHRAAEFRLKLQGVSYADIAKSGGGILST FT VQMTRDASEEELIDQSLPRLLALKNEGVTTVEIKSGYGLDLQNELKMLKVARQLGEMAG FT VRVKTTFLGAHAVGPEFKGNSQAYVDFLCNEMLPAAKNMDLVDTVDVFCESIAFSIRQA FT EQIFQAAKDLNLPIKCHAEQLSNMGASSLAARYGALSCDHLEFLDENGALNMVKANTVA FT VLLPGAFYFLKEKQKPPVDLLRQVGVGMAIATDSNPGSSPTTSLLLMMSMACQFFSMSI FT PEVLSAVTYQASRALGMEKDIGSIEAGKIADLVLWSIKDSAALCYYFAYPLPHQTMVAG FT EWVS MFACDELLLN ASTIDATGLQ LSNQAIVIKK GRIEWCGSED QLPAHFQESA KSRKDCHGQL 60 ITPGLIDCHT ...
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., ...
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 ...
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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 Nucleoporin 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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