Immunologic techniques based on the use of: (1) enzyme-antibody conjugates; (2) enzyme-antigen conjugates; (3) antienzyme antibody followed by its homologous enzyme; or (4) enzyme-antienzyme complexes. These are used histologically for visualizing or labeling tissue specimens.
Histochemical localization of immunoreactive substances using labeled antibodies as reagents.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
The portion of an interactive computer program that issues messages to and receives commands from a user.
Databases devoted to knowledge about specific genes and gene products.
Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
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.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Sequential operating programs and data which instruct the functioning of a digital computer.
Extensive collections, reputedly complete, of references and citations to books, articles, publications, etc., generally on a single subject or specialized subject area. Databases can operate through automated files, libraries, or computer disks. The concept should be differentiated from DATABASES, FACTUAL which is used for collections of data and facts apart from bibliographic references to them.
Organized activities related to the storage, location, search, and retrieval of information.
Software designed to store, manipulate, manage, and control data for specific uses.
Instrumentation consisting of hardware and software that communicates with the BRAIN. The hardware component of the interface records brain signals, while the software component analyzes the signals and converts them into a command that controls a device or sends a feedback signal to the brain.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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 procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The mixture of gases present in the earth's atmosphere consisting of oxygen, nitrogen, carbon dioxide, and small amounts of other gases.
Characteristics or attributes of the outer boundaries of objects, including molecules.
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).
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Specific languages used to prepare computer programs.
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.
Methods for determining interaction between PROTEINS.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The systematic study of the complete DNA sequences (GENOME) of organisms.
A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Specifications and instructions applied to the software.
The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).
A system in which the functions of the man and the machine are interrelated and necessary for the operation of the system.
Databases devoted to knowledge about specific chemicals.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)
Works about clinical trials that involve at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.
Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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)
Systems where the input data enter the computer directly from the point of origin (usually a terminal or workstation) and/or in which output data are transmitted directly to that terminal point of origin. (Sippl, Computer Dictionary, 4th ed)
The terms, expressions, designations, or symbols used in a particular science, discipline, or specialized subject area.
Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.
Activities performed to identify concepts and aspects of published information and research reports.
Computer-based representation of physical systems and phenomena such as chemical processes.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
The relationships of groups of organisms as reflected by their genetic makeup.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Computer-based systems for input, storage, display, retrieval, and printing of information contained in a patient's medical record.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Computerized compilations of information units (text, sound, graphics, and/or video) interconnected by logical nonlinear linkages that enable users to follow optimal paths through the material and also the systems used to create and display this information. (From Thesaurus of ERIC Descriptors, 1994)
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Systems composed of a computer or computers, peripheral equipment, such as disks, printers, and terminals, and telecommunications capabilities.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The thermodynamic interaction between a substance and WATER.
The adhesion of gases, liquids, or dissolved solids onto a surface. It includes adsorptive phenomena of bacteria and viruses onto surfaces as well. ABSORPTION into the substance may follow but not necessarily.
Databases devoted to knowledge about PHARMACEUTICAL PRODUCTS.
The testing of materials and devices, especially those used for PROSTHESES AND IMPLANTS; SUTURES; TISSUE ADHESIVES; etc., for hardness, strength, durability, safety, efficacy, and biocompatibility.
An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Computer processing of a language with rules that reflect and describe current usage rather than prescribed usage.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.
The visual display of data in a man-machine system. An example is when data is called from the computer and transmitted to a CATHODE RAY TUBE DISPLAY or LIQUID CRYSTAL display.
A publication issued at stated, more or less regular, intervals.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
The accumulation of an electric charge on a object
Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.
The characteristic three-dimensional shape of a molecule.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Elements of limited time intervals, contributing to particular results or situations.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Equipment that provides mentally or physically disabled persons with a means of communication. The aids include display boards, typewriters, cathode ray tubes, computers, and speech synthesizers. The output of such aids includes written words, artificial speech, language signs, Morse code, and pictures.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Evaluation undertaken to assess the results or consequences of management and procedures used in combating disease in order to determine the efficacy, effectiveness, safety, and practicability of these interventions in individual cases or series.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Proteins found in any species of bacterium.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
An approach of practicing medicine with the goal to improve and evaluate patient care. It requires the judicious integration of best research evidence with the patient's values to make decisions about medical care. This method is to help physicians make proper diagnosis, devise best testing plan, choose best treatment and methods of disease prevention, as well as develop guidelines for large groups of patients with the same disease. (from JAMA 296 (9), 2006)
Integrated, computer-assisted systems designed to store, manipulate, and retrieve information concerned with the administrative and clinical aspects of providing medical services within the hospital.
An agency of the NATIONAL INSTITUTES OF HEALTH concerned with overall planning, promoting, and administering programs pertaining to advancement of medical and related sciences. Major activities of this institute include the collection, dissemination, and exchange of information important to the progress of medicine and health, research in medical informatics and support for medical library development.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
Artificially produced membranes, such as semipermeable membranes used in artificial kidney dialysis (RENAL DIALYSIS), monomolecular and bimolecular membranes used as models to simulate biological CELL MEMBRANES. These membranes are also used in the process of GUIDED TISSUE REGENERATION.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Published materials which provide an examination of recent or current literature. Review articles can cover a wide range of subject matter at various levels of completeness and comprehensiveness based on analyses of literature that may include research findings. The review may reflect the state of the art. It also includes reviews as a literary form.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Copies of a work or document distributed to the public by sale, rental, lease, or lending. (From ALA Glossary of Library and Information Science, 1983, p181)
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Methods of creating machines and devices.
... showing that protein complexes assemble via distinct, ordered pathways. She showed that these assembly pathways are conserved ... Her databases and computational analysis methods have had a broad and deep impact on the community. She represents a new breed ... of scientists at the interface between computational and experimental molecular biology. Teichmann has also been an activist ... higher order protein structure and protein folding, and the principles underlying protein complex formation and organization. ...
The cofactor bound can be either Mg2+ or Ni2+ (Protein Database). As previously mentioned it is involved in the biosynthesis of ... The active enzyme complex is formed by two trimers in a head-to-head fashion. The active site is in between the trimer-trimer ... Another diagnostic method is to measure Pteridine levels in urine and to measure neurotransmitters 5-hydroxyindolacetic acid (5 ... we must look at the BH4 synthesis pathway. PTPS is an intermediate in this cycle and is needed to convert 7,8 - ...
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. SynechoNET is ... As noted above in RNA Polymerase and Sigma Factors, the beta clamp proteins within the RNAP complex have a higher initial ... PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein". PLOS ONE. 8 (2): e56470. Bibcode: ... The original method was to grow cyanobacteria for the biomass, which could be converted through liquefaction into liquid fuel. ...
... protein and complexes of these. The interaction can be direct or indirect (through transcribed RNA or translated protein). In ... The Drosophila Hippo signaling pathway provides a good example. The Hippo signaling pathway controls both mitotic growth and ... Plant Transcription Factor Database and Plant Transcriptional Regulation Data and Analysis Platform Open source web service for ... Nodes that are depicted as lying along vertical lines are associated with the cell/environment interfaces, while the others are ...
... pathway, which requires a membrane-bound Tat complex and the pH gradient as an energy source. Some other proteins are inserted ... Additional low-abundance lumenal proteins can be predicted through computational methods. Of the thylakoid proteins with known ... Plastid Protein Database Peltier J, Friso G, Kalume D, Roepstorff P, Nilsson F, Adamska I, van Wijk K (2000). "Proteomics of ... in wide sheets perpendicular to the grana stack axis and form multiple right-handed helical surfaces at the granal interface. ...
Other molecular pathway databases GeneNetwork Panther Pathways Pathway Commons. ... Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological ... Croft, D (2013). Building models using Reactome pathways as templates. Methods in Molecular Biology. 1021. pp. 273-83. doi: ... Uniprot and ChEBI accessions are preferred but the interface will accept and interpret many other identifiers or symbols. Mixed ...
... the atomic details of binding interfaces and produce detailed atomic models of protein-protein complexes[20][21] as well as ... In fact, any method has built in biases, especially protein methods. Because every protein is different no method can capture ... as in a signaling pathway, or structural, as in a protein complex. In fact, it is a formidable task to identify protein ... A Protein-Protein Interaction Database for Maize". Plant Physiology. 170 (2): 618-626. doi:10.1104/pp.15.01821. ISSN 1532-2548 ...
An Ontology-Based Pathway Database Coupled with Data Analysis Tools". Protein Networks and Pathway Analysis. Methods in ... gene expression profiles and protein-protein interactions into an interface called Bioinformatics Workbench, which is accessed ... single-genome data view can also show a protein-protein interaction browser that allows the inspection of interaction complexes ... button initiates a pathway browser that illustrates the complete pathways of all organisms in the MicrobesOnline database. In ...
A Cochrane database study suggests that blood loss and the risk of postpartum bleeding will be reduced in women offered active ... The end pathway of both mechanisms leads to contractions in the myometrium, a mechanical cause of placental separation, which ... In the seventh month of pregnancy the MHC-I complexes increase in the interplacentomal arcade reduces the bi- and tri-nucleate ... Methods of active management include umbilical cord clamping, stimulation of uterine contraction and cord traction. Active ...
... protein complex composition, wild type / mutant information), kinetic parameters together with corresponding rate equation, ... SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information ... Methods in Systems Biology. Methods in Enzymology. 500. pp. 215-231. doi:10.1016/B978-0-12-385118-5.00012-8. ISBN 978-0-12- ... SABIO-RK offers several ways for data access: a browser-based interface RESTful-based web services for programmatic access ...
Perform a BLAST search against plasmid-specific BLAST databases containing genomic sequences or proteins in PATRIC. Perform ... Comparative pathways: Compares consistently annotated metabolic pathways across closely related or diverse groups of genomes ... and databases required to support them. It also conducts research by applying its methods and data to make new discoveries of ... The freely available PATRIC platform provides an interface for biologists to discover data and information and conduct ...
"Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants". Nucleic Acids ... methods, but these methods are laborious and can only capture a tiny subsection of a transcriptome. Consequently, the manner in ... The most up to date and complex way to measure aging rate is by using varying biomarkers of human aging is based on the ... Most popular RNA-Seq programs are run from a command-line interface, either in a Unix environment or within the R/Bioconductor ...
positive regulation of protein kinase B signaling. • negative regulation of Notch signaling pathway. • regulation of JAK-STAT ... EGF at the Human Protein Reference Database.. *Epidermal+growth+factor at the US National Library of Medicine Medical Subject ... receptor complex. • extracellular region. • lysosomal membrane. • extracellular exosome. • platelet alpha granule lumen. • ... synthetic scaffolds for manufacturing of bioengineered grafts by emulsion electrospinning or surface modification methods.[20][ ...
Cyclooxygenase pathway may generate the free radicals since ibuprofen blocked as well the ANTU damage. ANTU causes local ... The usual method is the reaction of 1-naphthylamine hydrochloride with ammonium thiocyanate: [C10H7NH3]Cl + NH4SCN → C10H7NHC(S ... As a result, the formation of hydrodisulfide complexes takes place (R-S-S-H). This compound is very likely to react with ... 2001-145 (CD-ROM) August 2001 Govers H et al; Chemosphere 15: 383-93 (1986) US EPA; Estimation Program Interface (EPI) Suite. ...
She compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence ... signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these ... This system allows the database to be accessed and updated by all experts in the field. SOAP- and REST-based interfaces have ... without performing protein-protein interaction experiments. A variety of methods have been developed to tackle the protein- ...
A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods. ... Camacho CJ, Vajda S (2008). "Protein docking along smooth association pathways". Proceedings of the National Academy of ... Esmaielbeiki R, Nebel JC (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15: ... structural families according to the SCOP database. Benchmark elements are classified into three levels of difficulty (the most ...
Pitfalls: The raison d'etre for these complex methods is to avoid the myriad of pitfalls that can lead to statistical errors ... in this case the overlap between differentially expressed genes and gene sets from known pathways/databases (e.g., Gene ... Gene expression is often used as a proxy for protein abundance, but these are often not equivalent due to post transcriptional ... Common tools for gene set enrichment include web interfaces (e.g., ENRICHR, g:profiler) and software packages. When evaluating ...
The databases established by CGAP continues to contribute to knowledge of cancers in terms of their pathways and progression. ... The MGC provides researchers with full-length protein information from cDNA, unlike EST or SAGE databases which only provide ... Therefore, an improved method called serial analysis of gene expression (SAGE) is also used. This method identifies, for each ... identify alternate forms of genes and analyze complex molecular pathways that regulate cell metabolism, growth, or ...
There are databases dedicated to SNPs (dbSNP), the knowledge on genes characterization and their pathways (KEGG) and the ... "Statistical Methods in Medical Research". SAGE Journals.. *^ "Pharmaceutical Statistics - Wiley Online Library". onlinelibrary. ... Frank Emmert-Streib; Matthias Dehmer (2010). Medical Biostatistics for Complex Diseases. Wiley-Blackwell. ISBN 978-3-527-32585- ... Another possibility is search for the desired term (a gene, a protein, a disease, an organism, and so on) and check all results ...
The complex phenotypes of several disorders are suspected to be caused by the involvement of moonlighting proteins. The protein ... Furthermore, moonlighting proteins appear to be abundant in all kingdoms of life. Various methods have been employed to ... Enzyme promiscuity Pseudoenzymes Media related to Moonlighting proteins at Wikimedia Commons database ... However, unlike lens, cornea depends on the air-cell interface and its curvature for refraction. Early immunology studies have ...
... querying and visualization of gene regulation and protein interaction networks, metabolic and signaling pathways. WZL Gear ... It serves as a graphical user interface (GUI) to the R-package TIMP, which is the computational engine of Glotaran. It works ... EasyDoe Toolsuite, by IAV in Berlin, Germany, provides a workflow for control units of calibration engines, using a method ... SkyRoad Swap Trader provides consolidated real-time analytics for the rates trading complex including CCP, traditional OTC and ...
... "co-complex" methods. Homo-oligomers are macromolecular complexes constituted by only one type of protein subunit. Protein ... Protein-Protein Interaction Databases Library of Modulators of Protein-Protein Interactions (PPI) Proteins and Enzymes at ... Janin J (December 1999). "Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition". ... basing their functionalities on the theory that proteins involved in common pathways co-evolve in a correlated fashion across ...
I. Isolation and characterization of the protein-glycogen complex". Journal of Biological Chemistry. 245 (24): 6642-6648. PMID ... First, the catalytic sites are relatively buried, 15Å from the surface of the protein and from the subunit interface.[6] This ... The inhibition of glycogen phosphorylase has been proposed as one method for treating type 2 diabetes.[10] Since glucose ... metabolic pathway. PRIAM. profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. ...
These maps utilize databases such as BioGRID and the Human Protein Reference Database. The metabolic network encompasses the ... Journal of the Royal Society Interface, 2(4), 295-307. Pastor-Satorras, R., & Vespignani, A. (2002). Immunization of complex ... Biological networks, such as protein-protein interactions and metabolic pathways, are utilized by network medicine. Disease ... method. This states if two diseases are treated by the same drug, a drug that treats one disease may treat the other. Drug ...
... at the Encyclopædia Britannica NCBI Entrez Protein database NCBI Protein Structure database Human Protein Reference Database ... Keskin O, Tuncbag N, Gursoy A (April 2008). "Characterization and prediction of protein interfaces to infer protein-protein ... Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. ... Many structure prediction methods have served to inform the emerging field of protein engineering, in which novel protein folds ...
Disulfide bond formation protein (DsbA-DsbB complex). Proteins with alpha-helical transmembrane anchors[edit]. *T cell receptor ... Due to this difficulty and the importance of this class of proteins methods of protein structure prediction based on hydropathy ... See also: Transporter Classification Database. Light absorption-driven transporters[edit]. *Bacteriorhodopsin-like proteins ... while the rest of the protein is situated at the micelle-water interface and can adopt different types of non-native ...
"BioModels Database - A Database of Annotated Published Models". Retrieved 23 March 2012. "Pathway Commons". Retrieved 23 March ... The graphical user interface allows construction of complex models in biologically relevant terms: compartment dimensions and ... Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM (2012). "Spatial modeling of cell signaling networks". Methods in Cell ... Model elements can be annotated with IDs from Pubmed UniProt (proteins) KEGG (reactions and species) GeneOntology (reactions ...
The project involves: Databases: 3D reconstructed model neurons, synapses, synaptic pathways, microcircuit statistics, computer ... An artificial neural network described as being "as big and as complex as half of a mouse brain" was run on an IBM Blue Gene ... Methods in Molecular Biology. 401. Totowa, NJ: Humana. ISBN 978-1-58829-720-4. OCLC 123798711. Koslow, Stephen H.; Huerta, ... Research on brain-computer interface began in the 1970s at the University of California, Los Angeles under a grant from the ...
Further information: Iron-sulfur protein. Iron-sulfur clusters are complexes of iron and sulfur atoms held within proteins by ... A computational method, IPRO, recently predicted mutations that experimentally switched the cofactor specificity of Candida ... Hanukoglu I (December 2017). "Conservation of the Enzyme-Coenzyme Interfaces in FAD and NADP Binding Adrenodoxin Reductase-A ... linked metabolic pathways such as the citric acid cycle and the synthesis of ATP.[76] ...
... showing that protein complexes assemble via distinct, ordered pathways. She showed that these assembly pathways are conserved ... Her databases and computational analysis methods have had a broad and deep impact on the community. She represents a new breed ... of scientists at the interface between computational and experimental molecular biology. Teichmann has also been an activist ... higher order protein structure and protein folding, and the principles underlying protein complex formation and organization. ...
... a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional ... Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes ... and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in ... interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models. ...
Next message: [Computational-biology] Reactome Pathway Database User Survey * Messages sorted by: [ date ] [ thread ] [ subject ... This course is designed to demonstrate the use of computational methods to determine the most likely structure of the complex ... formed by interacting proteins, identify potentially druggable sites in the interface, determine whether the target is ... The problem of disrupting protein-protein interactions . Predicting the structure of protein-protein complexes using fragment- ...
However such methods are far less tractable for holistic cellular models, which are instead represented at the level of network ... The complex environment of a living cell contains many molecules interacting in a variety of ways. Examples include the ... One very interesting hypothesis has been generated regarding the regulation of yeast glycolysis by a protein found to interact ... Sophisticated dynamic modelling approaches provide detailed knowledge about single processes or individual pathways. ...
The characterization of complex biological systems based on high-throughput protein quantification through mass spectrometry ... Proteins / genetics* * Proteomics / methods * Proteomics / statistics & numerical data* * Software* * User-Computer Interface ... The characterization of complex biological systems based on high-throughput protein quantification through mass spectrometry ... such as PSEA-Quant and Reactome pathway analysis, for data set enrichment analysis. PINT serves as a centralized hub for large- ...
Protein-protein docking algorithms are powerful computational tools, capable of analyzing the protein-protein interactions at ... Protein-Protein Docking: Are We There Yet?: 10.4018/978-1-5225-1762-7.ch042: ... a three dimensional structure of such protein complexes is an essential step toward identifying their binding interface and ... A simple comparison between protein structure and gene sequence databases would simply reveal the great discrepancy between the ...
... and that the interface used in this homodimeric complex is very similar to that used in the formation of heterodimer. In ... protein that forms heterodimeric transcriptional regulator complexes with several other bHLH-PAS subunits to control a variety ... One of these is the hypoxia response pathway, which allows eukaryotic cells to respond to low oxygen tension via the formation ... You may read the explanation of the method and the full data available from ConSurf. ...
... the authors present an integrated mass spectrometry-based approach that allows them to define the Drosophila RNA-protein ... Comprehensive characterisation of RNA-protein interactions requires different levels of resolution. Here, ... Dzieciatkowska, M., Hill, R. & Hansen, K. C. GeLC-MS/MS analysis of complex protein mixtures. Methods Mol. Biol. 1156, 53-66 ( ... The InterPro protein families database: the classification resource after 15 years. Nucl. Acids Res. 43, D213-D221 (2015). ...
... we examined the protein-protein interface of 212 complexes from our exhaustive database, keeping in mind the difficulties in ... Methods. The wrapping of backbone (amide-carbonyl) hydrogen bonds by side-chain carbonaceous groups (CHn, n = 1, 2, 3) ... Are most backbone hydrogen bonds thoroughly dehydrated along a folding pathway? (iii) What are the implications of individual ... Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface ...
... a database of 86 intramolecular complexes was built from the PSIMAP database (34) following the protocol described in Methods ... interactions hold the cell machineries and govern the flow of information transmitted through cell signaling pathways. To ... 2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13:190-202. ... 1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35:364-373. ...
... throughput experiments to measure protein-protein interactions has created a flood of proteomic information parallel to the ... Protein-protein interaction databases may include both complexes between proteins and purely functional associations. This ... Predicted GO pathways are also available (not shown).. Figure 4. Comparison of PPI interfaces and small molecule binding ... Here, we review the main methods to characterise protein interactions in vitro and in vivo, the methods by which protein ...
... occurs at a conserved groove on a face of the protein that is distinct from the G-protein interface of classical RGS proteins. ... I-mfa domain proteins interact with Axin and affect its regulation of the Wnt and c-Jun N-terminal kinase signaling pathways. ... Also component of the AXIN1-HIPK2-TP53 complex which controls cell growth, apoptosis and development.[26] [27] [28] [APC_HUMAN ... You may read the explanation of the method and the full data available from ConSurf. ...
... protein, reaction and pathway. We used WholeCellKB to create WholeCellKB-MG, a comprehensive database of the Gram-positive ... NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, ... Database issue): D787-92 Abstract. Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors ... Accelerated discovery via a whole-cell model Nature Methods. Sanghvi, J. C., Regot, S., Carrasco, G. S., Karr, J. R., Gutschow ...
... complexes. A computer approach was developed to analyze the surface of peptides and proteins using a level set method which ... and protein-antibody complexes have been investigated. Datasets were constituted from the IMGT database and consisted of 37 ... protein kinase C pathway, pro-inflammatory cytokines and various growth factors. Angiotensin II and transforming growth factor ... of small molecules to specifically control important cellular functions is an area of major current interest at the interface ...
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat Genet ... Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014; 42(Database issue):D7D17. (12 ... of methods to analyze large complex data sets, such as those produced by the application of microarray (40) or RNA sequencing ( ... A novel clinician interface to improve clinician access to up-to-date genetic results. J Am Med Inform Assoc. 2013; 21: e117- ...
MATERIALS AND METHODS. Sequence annotation. The computational pipeline underlying the construction of the CLIPZ database takes ... Because the Argonaute/EIF2C proteins that are part of the RNA-induced silencing complex have been a major focus of the CLIP ... Insulin-like growth factor II mRNA-binding proteins 1-3). The data are presented through a web interface that supports not only ... mirbase/CURRENT were included to be able to analyze data specific to proteins involved in the miRNA-dependent silencing pathway ...
Structure/function studies of a plant pathogen effector in complex with a host disease resistance protein domain reveal the ... The structure of the Pikp-HMA/AVR-PikD complex reveals an intimate interface formed between these proteins that buries 18.7% of ... Materials and methods. Gene cloning: heterologous protein production, Y2H, fungal transformation and in planta expression. For ... Database searches using PDBeFold reveals that a close structural homologue of AVR-PikD is AVR-Piz-t (Zhang et al., 2013), ...
Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 ... In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction ... The method groups topologically similar proteins under this measure in a PPI network and shows that these protein groups belong ... The results are displayed via a visual interface for easy perusal. The server is available at ...
... protein & metabolite expression Protein sequences, families & motifs Chemical biology Reactions, interactions & pathways IntAct ... Atlas Ligand induced transcript response 750 PDBe Ligand structures from protein complexes 15K ChEBI Nomenclature of primary ... granted JP Abstracts Patent Offices Chemistry Database SureChEMBL System Patent PDFs (service) Application Users API Database ... one method) Name to Structure (five methods) OCR Processed patents (service) ...
... pathway, and/or protein complex (Costanzo et al. 2010, 2016). ... The web interface is developed using a combination of HyperText ... 2014 Synthetic genetic array analysis for global mapping of genetic networks in yeast. Methods Mol. Biol. 1205: 143-168. ... a protein complex standard (Costanzo et al. 2016), and two different protein localization standards (Huh et al. 2003; Koh et al ... genes are grouped into modules corresponding to protein complexes and pathways. At an intermediate level of network resolution ...
... a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein ... Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol ... Lua RC, Lichtarge O (2010) PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes ... Revell LJ (2013) Rphylip: an R interface for PHYLIP. R package (Version 0-1.09)Google Scholar ...
I want to investigate experimentally in which order the interfaces of protein complexes are formed and to which extent ... I want develop methods to systematically screen for additional factors involved in assembly pathways. I furthermore want to ... By explicitly utilizing cores, I will be able to build a powerful computational database engine that scales the entire spectrum ... Summary Protein complexes are central to many cellular functions but our knowledge of how cells assemble protein complexes ...
Background Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and ... Two major types of biological pathways could be distinguished. Metabolic pathways incorporate complex networks of protein-based ... assessing pathway databases. Thus, biomedical scientists have to make their choice of the database based on interface, prior ... If not, why are they not there and why the method used by the authors is better than the ones used by the database teams to ...
It uses the crystal symmetry operators and a method of scoring each trial protein-protein interface. ... PDBsum is a pictorial database providing an at-a-glance overview of the contents of each 3D structure deposited in the Protein ... NetEffects analyse the effects of perturbations to specific pathway components on the rest of the pathway, and especially the ... to identify small molecules that might form a complex with the protein. The server uses resources such as ChEMBL, ChEBI and the ...
For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 ... These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. ... The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore ... are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions ...
... so understanding protein-protein interactions means coming deeply into the functional role of proteins in life ... The amazing variety of protein functions are often covered by protein complexes, ... Keywords: protein-protein interactions; hotspots; protein-protein interface; computational methods; network pharmacology; drug ... The analysis of protein-protein interfaces is crucial to quantify protein complex stability. ...
... a critical effector of the ERK signaling pathway, is hyperactivated in many cancers. Oncogenic BRAFV600E signals as an active ... Protein residues lining the base of αC-helix and HRD motif are shown in surface representation. Protein-ligand interface ... Coordinates have been deposited with the Protein Data Bank (BRAFV600E-PON complex: PDB 6P3D, BRAFV600E-PHI1 complex: PDB 6P7G). ... This pathway is normally activated by receptor tyrosine kinase signaling that stimulates binding of GTP to RAS at the plasma ...
... for significant manual labor when working with huge lists of SNPs and that algorithms work only for SNPs present in databases ... The mature miRNA together with the protein-silencing complex (RISC) seeks and binds to mRNA at target sites. Binding can cause ... 57 of the 64 pairs queried are present in the PolymiRTS database, which includes miRNA-mRNA pairs identified through methods ... Moreover, if the list of SNPs is large, the web interface of the tools may require an infeasible amount of manual labor. With ...
Macromolecular crystallography and structural biology databases at NIST.(National Institute of Standards and Technology) by ... This inconsistency reflects the evolution of experimental methods, functional knowledge of proteins, and methods used to ... 30.) I. T. Weber and T. A. Steitz, Structure of a Complex of Catabolite Gene Activator Protein and Cyclic AMP Refined at 2.5 [ ... Mature subtilisin represents a class of proteins that lacks an efficient folding pathway. Refolding of mature subtilisin BPN ...
The cofactor bound can be either Mg2+ or Ni2+ (Protein Database). As previously mentioned it is involved in the biosynthesis of ... The active enzyme complex is formed by two trimers in a head-to-head fashion. The active site is in between the trimer-trimer ... Another diagnostic method is to measure Pteridine levels in urine and to measure neurotransmitters 5-hydroxyindolacetic acid (5 ... we must look at the BH4 synthesis pathway. PTPS is an intermediate in this cycle and is needed to convert 7,8 - ...
  • From 2001-2012, she was a Medical Research Council (MRC) Programme Leader, studying patterns in protein interactions and transcriptional regulatory networks. (
  • Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. (
  • About the course: Despite the growing number of examples of small molecule inhibitors that disrupt protein-protein interactions (PPIs), the origin of druggability is poorly understood. (
  • Protein-protein docking algorithms are powerful computational tools, capable of analyzing the protein-protein interactions at the atomic-level. (
  • Protein-protein interactions play key roles in several biological processes. (
  • All these processes are mediated by selective and potent protein-protein interactions (Waksman & Sansom, 2005). (
  • Furthermore, many diseases have been associated with either an over-activated or an under-regulated protein-protein interaction and the cure for these diseases has been focused on either inhibiting or stimulating these interactions, respectively. (
  • Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. (
  • Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein-protein complex structures. (
  • Combinations of inter- and intramolecular interactions hold the cell machineries and govern the flow of information transmitted through cell signaling pathways. (
  • In the context of evolution, seminal studies compared the binding modes of domain-domain interactions between homologous proteins and concluded that they tend to interact similarly, even if sequence identity has been maintained as low as 30% ( 15 , 16 ). (
  • The advent of high‐throughput experiments to measure protein-protein interactions has created a flood of proteomic information parallel to the influx of data caused by the advent of next‐generation sequencing technologies. (
  • Here, we review the main methods to characterise protein interactions in vitro and in vivo , the methods by which protein networks are constructed and the characteristics of the major protein interaction databases, and the techniques used to predict the functional impact of mutations on protein interaction networks. (
  • Protein-protein interactions are the driving force for cellular responses and disruption of protein-protein interfaces. (
  • High‐throughput techniques to measure protein interactions in vivo are prone to both high false‐positive and high false‐negative rates. (
  • Each method of identifying protein interactions has systematic errors associated with it that can be partly corrected by cross validating the results with two techniques. (
  • Such dehydration-based hydrophobic interactions enhance the role of nearby intramolecular hydrogen bonds in stabilizing protein conformations ( 5 - 9 ) and facilitating the folding process (refs. (
  • Such hot spots enhance the contribution of hydrophobic interactions and contribute to defining binding sites, nucleating sites for aggregation, and protein reactivity in general. (
  • While protein-protein interactions (PPI) have been used widely to ident. (
  • These maps store wide knowledge of complex molecular interactions and regulations occurring in the living organism in a simple and obvious way, often using intuitive graphical notation. (
  • It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. (
  • The amazing variety of protein functions are often covered by protein complexes, so understanding protein-protein interactions means coming deeply into the functional role of proteins in life. (
  • In the last years, the investigation of protein-protein interactions has become central in many fields, spanning from molecular biology to pharmacology. (
  • Protein-protein interactions underlie several physiological mechanisms. (
  • Network‐based approaches clarify the multiscale nature of protein-protein interactions. (
  • Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. (
  • Interactions between proteins can be direct physical interactions and also indirect, which may involve intermediate molecules to facilitate interactions. (
  • For example, an indirect interaction means that if proteins A and B, and also B and C, have direct interactions, then A and C indirectly interact. (
  • Comparative proteomic analysis software suite is designed to better assess the confidence level of proteinΠprotein interactions that are not well-suited for the analysis of large nonreciprocal parallel data sets (e.g. antibody pull downs and identification of interacting proteins by MS/MS). CompPASS includes components that store, organize, and process data, and these components are linked to networking and functional-analysis tools. (
  • Gut microorganisms are the source of many bioactive products that play key functions in human host pathways and microbe-microbe interactions [2]. (
  • Protein-protein interactions ( PPI s) are essential to almost all cellular processes. (
  • To better understand the relationships of proteins in Arabidopsis ( Arabidopsis thaliana ), we have developed a genome-wide protein interaction network (AraPPINet) that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins. (
  • AraPPINet exhibited high predictive power for discovering protein interactions at a 50% true positive rate and for discriminating positive interactions from similar protein pairs at a 70% true positive rate. (
  • Experimental evaluation of a set of predicted PPI s demonstrated the ability of AraPPINet to identify novel protein interactions involved in a specific process at an approximately 100-fold greater accuracy than random protein-protein pairs in a test case of abscisic acid ( ABA ) signaling. (
  • Protein-protein interactions ( PPI s) are essential to almost all cellular processes, including DNA replication and transcription, signal transduction, and metabolic cycles. (
  • for uncovering protein interactions over the past decade. (
  • According to an empirical estimation of the size of the protein interactome, experimentally determined interactions represent a small fraction (approximately 6%) of the entire protein interactome, and the relationships among most proteins remain to be discovered ( Arabidopsis Interactome Mapping Consortium, 2011 ). (
  • ConsensusPathDB integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. (
  • Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions. (
  • it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases. (
  • Binary protein interactions are scored with our confidence assessment tool, IntScore. (
  • ConsensusPathDB is a meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. (
  • Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. (
  • With 155,432 human, 194,480 yeast and 13,648 mouse complex functional interactions (originating from 18 databases on human and eight databases on yeast and mouse interactions each), ConsensusPathDB currently constitutes the most comprehensive publicly available interaction repository for these species. (
  • The Web interface at offers different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways. (
  • ConsensusPathDB is a database system for the integration of human functional interactions. (
  • Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. (
  • ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26,133 distinct physical entities and 74,289 distinct functional interactions (protein-protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. (
  • It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. (
  • or between small molecules and proteins [1] ) but can also describe sets of indirect interactions among genes ( genetic interactions ). (
  • The interactomes based on PPIs should be associated to the proteome of the corresponding species in order to provide a global view ("omic") of all the possible molecular interactions that a protein can present. (
  • Molecular interactions can occur between molecules belonging to different biochemical families (proteins, nucleic acids, lipids, carbohydrates, etc.) and also within a given family. (
  • For instance, the Sirt-1 protein interactome and Sirt family second order interactome [5] [6] is the network involving Sirt-1 and its directly interacting proteins where as second order interactome illustrates interactions up to second order of neighbors (Neighbors of neighbors). (
  • [8] Although protein-protein interaction maps containing several thousand binary interactions are now available for several species, none of them is presently complete and the size of interactomes is still a matter of debate. (
  • The yeast interactome, i.e. all protein-protein interactions among proteins of Saccharomyces cerevisiae , has been estimated to contain between 10,000 and 30,000 interactions. (
  • ADME DB -- ADME DB is a database containing the latest and most comprehensive data on interactions of substances with Drug Metabolizing Enzymes and Drug Transporters. (
  • Homooligomeric states may be conserved within certain protein subfamilies and might be important in providing specificity to certain substrates while minimizing interactions with other unwanted partners. (
  • Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. (
  • Protein-protein interactions (PPIs) play a critical role in all cellular processes, ranging from cellular division to apoptosis. (
  • These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors. (
  • Protein-Protein Interactions (PPIs) play vital roles in most biological activities. (
  • As expected, proteins are mutually matched with each other, forming a huge and complex network of Protein-Protein Interactions (PPIs) [ 2 ]. (
  • The integration of a variety of datasets, including binary interactions, protein complexes, and expression profiles enables the identification of subnetworks that are active under certain conditions. (
  • Deciphering Protein-Protein Interactions. (
  • To understand the mechanisms of protein recognition at the molecular level and to unravel the global picture of protein interactions in the cell, different experimental techniques have been developed. (
  • Some methods characterize individual protein interactions while others are advanced for screening interactions on a genome-wide scale. (
  • Recent advances in high-throughput experimental methods for the identification of protein interactions have resulted in a large amount of diverse data that are somewhat incomplete and contradictory. (
  • As valuable as they are, such experimental approaches studying protein interactomes have certain limitations that can be complemented by the computational methods for predicting protein interactions. (
  • In this review we describe different approaches to predict protein interaction partners as well as highlight recent achievements in the prediction of specific domains mediating protein-protein interactions. (
  • With the use of genome-wide mapping of genetic interactions, we showed that the components of the tethering complex were functionally connected to phospholipid biosynthesis and calcium-signaling genes. (
  • Designing materials based on the molecular-scale interactions between these proteins will help generate new multifunctional protein alloy biomaterials with tunable properties. (
  • The characterization of complex biological systems based on high-throughput protein quantification through mass spectrometry commonly involves differential expression analysis between replicate samples originating from different experimental conditions. (
  • The aryl hydrocarbon receptor nuclear translocator (ARNT) is a promiscuous bHLH-PAS (Per-ARNT-Sim) protein that forms heterodimeric transcriptional regulator complexes with several other bHLH-PAS subunits to control a variety of biological pathways, some of which are centrally involved in disease initiation and/or progression. (
  • This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. (
  • The modular assembly of proteins is a key determinant in the regulation of biological systems. (
  • Our focus is on building computational models of complex biological processes, and using these models to guide an experimental program. (
  • The shift in focus to systems biology in the post-genomic era has generated further interest in PPINs and biological pathways. (
  • To date, such plans include complementing the chemical annotations with biological ones, covering genes, proteins, diseases and indications. (
  • Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. (
  • Recently the biological pathways have become a common and probably the most popular form of representing biochemical information for hypothesis generation and validation. (
  • Two major types of biological pathways could be distinguished. (
  • Each of these databases has its own structure, way of data storage and representation, and method for extracting and verifying biological knowledge. (
  • NetEffects analyse the effects of perturbations to specific pathway components on the rest of the pathway, and especially the biological processes it controls. (
  • Pita suggests the most likely biological unit for a given X-ray crystal structure of a protein. (
  • However, as early as in the 1990s, it was reported that there is another class of proteins, which have no well-defined structures under physiological conditions, but still have biological functions [ 1 , 2 ]. (
  • In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macromolecule Crystallization Database in 1989. (
  • The NIH acknowledges the overlap with computational biology: "the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral and social systems. (
  • Bioinformatics tools are required to create and evolve measurement platforms and data analysis methods to reach new biological insight. (
  • DEAD-box proteins function throughout the lifetime of cellular RNAs from synthesis to biological activity, and to inevitable decay ( 5 ). (
  • The developments and broader applications of these methods not only improve our standing of the mechanisms of biological processes but also facilitate the diagnosis and therapy. (
  • However, Gene Ontology is a controlled vocabulary designed to organize information for molecular function, biological processes and cellular components and thus does not directly reflect metabolic pathways. (
  • RNA methylation, biological function, disease, database, Web server and software, computational model RNA methylation Methylation is a form of alkylation in chemistry, which adds a methyl group on a substrate or substitutes the original atom or group. (
  • Biological databases related to microarray Gene Ontology KEGG Biocarta Reactome MSigDB Pathway enrichment analysis GSEA GSA Ingenuity Pathway Analysis (IPA) Motif finding. (
  • 1.2 KEGG Kyoto Encyclopedia of Genes and Genomes KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks in biological processes (PATHWAY database), the information about the universe of genes and proteins (GENES/SSDB/KO databases), and the information about the universe of chemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). (
  • In this paper we summarize the biological importance of homooligomeric assemblies, physico-chemical properties of their interfaces, experimental and computational methods for their identification and prediction. (
  • Protein Structures and Information Extraction from Biological Texts: The PASTA System. (
  • It provides researchers with convenient access to a comprehensive collection of biological pathways from multiple sources represented in a common language for gene and metabolic pathway analysis. (
  • Many computational methods used for analyzing biological systems do not make full use of available data and/or make strong assumptions that might not be realistic. (
  • Using mammalian cell signaling as case studies article also summarize how computational modeling yields insight about cell signaling pathways or how computational analyses of networks shed light on specific biological processes. (
  • Modularity exists in a variety of biological contexts, including protein complexes, metabolic pathways, signaling pathways, and transcriptional programs.Network topologies reveal dynamic properties that contribute to cellular functions. (
  • It enables scientists to compare data against a database of representative compound profiles to determine trends and differences for a range of applications, including long-term monitoring of water sources for contaminant identification, adulteration of food products and identification of potential doping agents in a biological matrix. (
  • She represents a new breed of scientists at the interface between computational and experimental molecular biology. (
  • To further elucidate the competitions and synergies ruling the molecular logic of these protein-protein interaction networks, a critical step relies on the structural characterization of the protein complexes. (
  • The prediction of binding sites and the understanding of interfaces associated with protein complexation remains an open problem in molecular biophysics. (
  • This is needed, for example, to assess the role of water removal in protein-ligand associations ( 13 , 14 ), molecular disease, and aggregation ( 15 , 16 ). (
  • Interaction modes and molecular surface properties for both peptide- and protein-antibody complexes have been investigated. (
  • These tools are available to perform different steps of any phylogenetic analysis including inference of phylogenetic trees and their visualization, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. (
  • At the molecular-scale, we will use optical tweezers to measure active torques generated by single molecules of the molecular myosin and the actin polymerizing protein formin. (
  • The most innovative approaches, based on complex network theory, shed a very bright light on future trends for protein-protein applications on drug design and on molecular therapy for diseases where protein association plays a pivotal role (misfolding). (
  • Molecular docking allows a fine analysis of protein-protein interface. (
  • Finally, by reverse engineering the functional relevance of differentially expressed genes with specific cellular pathways, putative genes acting as hubs, were identified, linking functionally disparate cellular processes in the context of traditional molecular description. (
  • Selvaraj and Singh [2] described the potential impact of DNA molecule on therapeutic application through selective recognition of molecular targets and pathways. (
  • Selective activation or inhibition of a particular protein function can help elucidate crucial molecular mechanisms and enables important advances in cell biology. (
  • Small-molecule controlled molecular systems also possess tremendous value in bioengineering and biomedical applications: activation of protein function allows the construction of protein switches and biosensor proteins, whereas inhibition of protein function contributes to the development of novel therapeutic agents. (
  • VAMMPIRE (Virtually Aligned Matched Molecular Pairs Including Receptor Environment) matched molecular pairs database for structure-based drug design and style and optimisation. (
  • Deciphering the nature of PPI s not only advances our understanding of gene function at the molecular level but also provides insight into complex cellular processes. (
  • The organization of metabolic pathways at the molecular level is expected to have several advantages, such as to increase local concentrations of the enzymes and their substrates, to improve channeling of intermediates into specific sub-pathways and to increase metabolic fluxes and sequestration of reactive intermediates (Jørgensen et al. (
  • Yet, knowledge of the composition, wiring, dynamics and associated signaling pathways of the corresponding molecular building blocks and associated protein networks remains very limited. (
  • The hair cell mechanotransduction (MET) channel complex is essential for hearing, yet it's molecular identity and structure remain elusive. (
  • Although the molecular identity and structure of the MET channel remains elusive, a growing body of evidence supports the hypothesis that the transmembrane channel-like 1 and 2 (TMC1 and TMC2) proteins are pore-forming subunits of the MET channel. (
  • Molecular dynamics simulations of the docked complexes show they form stable complexes. (
  • 12. Anil VS, Kavitha PG, Kuruvilla S, Kumar P & Mathew MK (2012) Measurement of Cytosolic Ion Concentrations in Live Cells Book Chapter in "Methods in Molecular Biology", F Maathuis ed, published by Humana Press, USA. (
  • Molecular docking analysis revealed that CAPE is capable of disrupting mortalin-p53 complexes. (
  • Molecular architecture of the inner ring scaffold of the human nuclear pore complex. (
  • Is it possible to understand the molecular structure and function of proteins and nucleic acids in enough detail to make accurate predictions about structure and function? (
  • More specifically, I still write and maintain computer programs of all types including large simulation packages and molecular graphics interfaces. (
  • We identified the Mmm1/Mdm10/Mdm12/Mdm34 complex as a molecular tether between ER and mitochondria. (
  • Further docking and molecular dynamics (MD) simulations identified in the RNA groove two NP-naproxen complexes of similar levels of interaction energy. (
  • RNA methylation and diseases: experimental results, databases, Web servers and computational models Chen, Xing;Sun, Ya-Zhou;Liu, Hui;Zhang, Lin;Li, Jian-Qiang;Meng, Jia 2017-11-18 00:00:00 Abstract Ribonucleic acid (RNA) methylation is a type of posttranscriptional modifications occurring in all kingdoms of life. (
  • and to link the network to databases of functional annotations. (
  • Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models. (
  • Sensitive conservation analyses have been proposed to detect functional sites within proteins ( 18 ⇓ - 20 ) and have further been used for the identification of protein-binding sites ( 21 ⇓ ⇓ ⇓ ⇓ - 26 ). (
  • Functional associations between genes can be inferred by bioinformatic approaches, but the results do not necessarily imply a physical interaction between proteins. (
  • Protein-protein interaction databases may include both complexes between proteins and purely functional associations. (
  • Several mutations of the gene are associated with phenotypic functional deficiency of protein C, and with the risk of developing venous thrombosis. (
  • ProCMD is an up-to-date interactive mutant database that integrates phenotypical descriptions with functional and structural data obtained by computational approaches. (
  • ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. (
  • In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. (
  • Dintor covers a wide range of frequently required functionalities, from gene identifier conversions and orthology mappings to functional annotation of proteins and genetic variants up to candidate gene prioritization and Gene Ontology-based gene set enrichment analysis. (
  • In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. (
  • Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. (
  • On the other hand, an increasingly request of studying the complex proteome is to combine quantification and functional analysis together to reveal the unexplored mechanism in the cells. (
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (
  • Recent developments include pathway analysis of metabolite lists, visualization of functional gene/metabolite sets as overlap graphs, gene set analysis based on protein complexes and induced network modules analysis that connects a list of genes through various interaction types. (
  • ConsensusPathDB--a database for integrating human functional interaction networks. (
  • The analysis of 13 allosteric proteins revealed that modules characterize experimentally identified functional regions. (
  • Based on the study of an additional functionally annotated dataset of 115 proteins, we propose that high-modularity modules include functional sites and are the basic functional units. (
  • Our method decomposes protein structures into modules, allowing the study of signal transmission between functional sites. (
  • Although experimental methods such as double mutant cycle analysis [ 10 ] have provided insights into allosteric communications, understanding the general principles of the transmission of information between distant functional surfaces remains a challenge in structural biology. (
  • The majority of human proteins does not work in isolation but take part in pathways, complexes and other functional modules. (
  • RNA is the intermediate molecule, which links genetic information contained in genes to its expression in functional proteins. (
  • Using this method the study was able to predict known gene functions better than any other genome-scale data set as well as adding functional information for genes that hadn't been previously described. (
  • We also find that hair cells are permeable to 3 kDa dextrans, and that dextran permeation requires TMC1/2 proteins and functional MET channels, supporting the presence of a large permeation pathway and the hypothesis that TMC1 is a pore forming subunit of the MET channel complex. (
  • Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. (
  • ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. (
  • This course is designed to demonstrate the use of computational methods to determine the most likely structure of the complex formed by interacting proteins, identify potentially druggable sites in the interface, determine whether the target is druggable, and provide information on potential ligands. (
  • They have emphasized that size, shape, and the physicochemical complementarities at the interfaces are key descriptors that could be used to develop computational methods able to predict protein-binding sites from sequences or structures ( 8 ⇓ ⇓ ⇓ ⇓ ⇓ - 14 ). (
  • However, none of these techniques has reached the 'black box' level and require careful consideration of the systematic errors in both the underlying experimental data and the computational methods to give reliable results. (
  • This is an introduction to the array of computational methods, many new but some old, that underlie popular software used today. (
  • A number of computational methods based on machine learning have been developed to facilitate the identification of novel PPIs. (
  • Therefore, the development of reliable computational methods which can improve the recognition efficiency has important significance [ 9 - 11 ]. (
  • Technological innovations in both data generation and computational methods may advance our understanding significantly. (
  • We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them. (
  • They may be constructed using web services within the toolkit together with those from other providers, and can be saved, shared and reused, allowing biologists to construct their own complex queries over various tools and datasets, or execute pre-constructed workflows designed by expert bioinformaticians. (
  • Datasets were constituted from the IMGT database and consisted of 37 peptide-antibody (PEPT) and 155 protein-antibody (PROT) complexes. (
  • Analysis of high-throughput genomic and proteomic datasets requires familiarity with the use of specialized tools and web servers, and heterogeneous, complex data from various databases. (
  • Although diverse computational techniques have been developed, existing methods have two key weaknesses: they overfit training datasets and they yield non-overlapping biomarkers that complicate clinical validation. (
  • For validation purposes, we performed a meta-analysis in Oncomine database in five sarcoma datasets. (
  • The proposed method achieves promising prediction performance when performed on the PPIs of Yeast , H . pylori , and independent datasets . (
  • Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization. (
  • Capturing how selection pressure acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. (
  • However, there is still a huge gap between the proteome-wide data accumulating and the available structural details of macromolecular complexes. (
  • A number of studies have tackled the large-scale analysis of protein-protein complexes from a structural perspective ( 3 ⇓ ⇓ ⇓ - 7 ). (
  • This is indeed the case, as can be inferred by examination (see below) of an exhaustive structural database consisting of 1,476 high-resolution (≤3 Å) entries free of sequence redundancies. (
  • Aloy P and Russell RB (2002) Interrogating protein interaction networks through structural biology. (
  • Macromolecular crystallography and structural biology databases at NIST. (
  • Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of "hypotheti cal" proteins to aid in assigning function. (
  • Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. (
  • 1. Introduction structural biology studies began at NIST in the late 1970s when it was recognized that neutron diffraction methods could be used to obtain novel information about the atomic structure of macromolecules, especially in its ability to elucidate hydrogen atom positions. (
  • Prerequisite for structural studies on G protein-coupled receptors is the preparation of highly concentrated, stable, and biologically active receptor samples in milligram amounts of protein. (
  • By utilizing structural information obtained through X-ray crystallography or NMR spectroscopy, these tools allow efficient and affordable examination of large small-molecule databases and provide quantitative evaluation of the likelihood that a given protein-ligand interaction occurs. (
  • the prediction is then based on the structural similarity of the two protein models to the template complex. (
  • Accordingly, metabolon definition could be extended to "Transient and dynamic supramolecular organization of cooperating, often consecutive enzymes of a metabolic pathway, which often is associated with structural elements of the cell (e.g. membrane, cytoskeleton) and non-enzymatic proteins. (
  • Although most structural studies with gal-1 have investigated its binding to simple carbohydrates, in particular lactose and N -acetyl-lactosamine, this view is limited, because gal-1 functions at the cell surface by interacting with more complex glycans that are heterogeneous in size and composition. (
  • Structural and nonstructural viral proteins, positive- and negative-sense viral RNA, and infectious virus particles were found to be associated with a distinct population of membranes separated by FFZE. (
  • Silencing of the expression of genes involved in cholesterol ( DHCR7 , CYP51A1 ) and fatty acid ( FASN ) synthesis, phosphatidylinositol ( PI4KIIIβ ) and inositol phosphate ( ITPR3 ) metabolism, and RNA helicase activity ( DDX23 ) significantly decreased the amounts of Yuc8 genomic and antigenomic RNA, synthesis of the structural protein VP90, and virus yield. (
  • ORF2 encodes a precursor structural polyprotein, named VP90 in the human astrovirus (HAstV) serotype 8 (HAstV-8) strain Yuc8, which is proteolytically processed to produce the final capsid viral proteins VP34, VP27, and VP25 through a precursor polypeptide named VP70. (
  • Search for structural similarity in proteins. (
  • In situ structural analysis of the human nuclear pore complex. (
  • Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. (
  • Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. (
  • freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. (
  • 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. (
  • 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. (
  • 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. (
  • The cellular proteins associated with this membrane population in infected and mock-infected cells were identified by tandem mass spectrometry. (
  • 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. (
  • Initial annotation ( 1 ) indicated that the human genome contains ~300 genes that encode proteins with an RNA-recognition motif (RRM). (
  • We stressed the multiscale nature of approaches, longing from genome‐wide analysis to the detailed study of protein-protein interface on single residues. (
  • Several software programs have been developed that utilize one or more of these methods to identify miRNA binding sites in the genome. (
  • In addition, researchers can probe complementary non-coding parts of the genome and profile relevant proteins and metabolites to seek new understanding and treatments of disease. (
  • ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. (
  • G protein-coupled receptors (GPCRs) play a central role in cell-cell communication and represent the largest group of membrane proteins with over 800 members in the human genome. (
  • Several steps in amino acid synthesis pathways are not annotated in the Desulfovibrio vulgaris genome. (
  • Next-generation methods for rapid whole-genome sequencing enable the identification of single-base-pair mutations in Drosophila by comparing a chromosome bearing a new mutation to the unmutagenized sequence. (
  • GEML is an open-standard XML format which enables exchanging data between a variety of gene expression systems including web-based genome databases. (
  • Equally important and challenging as genome annotation, is the subsequent classification of predicted genes into their respective pathways. (
  • New genomes must be manually integrated into a Pathway/Genome Database (PGDB), which in turn sets the basis for more complex queries and analyses. (
  • However, the significant resources required to implement genome information for Pathway Tools might not be readily available. (
  • Genome analysis of L. plantarum revealed a high proportion of regulatory proteins (8.5%), which is a typical feature of bacteria that can be found in diverse environments, such as Listeria monocytogenes and pseudomonads ( 17 , 34 ). (
  • Among the regulatory proteins, two putative arginine repressor genes were identified in the genome of strain WCFS1. (
  • In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. (
  • More importantly, to date there have been no prior genome-wide evaluation studies (that are based on genome-wide binding and gene expression assays) assessing pathway databases. (
  • The nucleoprotein (NP) binds the viral RNA genome and associates with the polymerase in a ribonucleoprotein complex (RNP) required for transcription and replication of influenza A virus. (
  • We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. (
  • CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. (
  • Here, we introduce CAPRI (Crosslinked and Adjacent Peptides-based RNA-binding domain Identification), a technique which enhances RBD discovery by simultaneously identifying both crosslinked peptides (in the immediate vicinity of the RNA-protein interface) and adjacent peptides (next to the crosslinked peptide) from the same sample. (
  • A computer approach was developed to analyze the surface of peptides and proteins using a level set method which allows the characterization of shape complementarity using surface curvature. (
  • It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. (
  • However, the NSAF method did not consider the shared peptides generated during the MS experiment [ 7 ]. (
  • 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. (
  • NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. (
  • PINT provides an extremely flexible query interface that allows advanced Boolean algebra-based data filtering of many different proteomics features such as confidence values, abundance levels or ratios, data set overlaps, sample characteristics, as well as UniProtKB annotations, which are transparently incorporated into the system. (
  • The proteomics and genomics communities increasingly perceive glycans as essential elements in physiological and pathological processes rather than as decorative elements of lipids and proteins. (
  • The ultimate result of a proteomics study is a list of proteins found to be present (or differentially present) at various cell physiological conditions. (
  • By searching through major proteomics journals, we have collected approximately 800 independent studies published recently, which reported about 1000 different protein lists. (
  • Based on this data, we developed a computational tool PLIPS (Protein Lists Identified in Proteomics Studies). (
  • Using statistical analyses PLIPS identifies recently published proteomics studies, which report protein lists that significantly intersects with a query list. (
  • Since the complex proteomes consist of a number of proteins with diversified functions, they pose a challenge for quantitative proteomics analysis. (
  • Speakers discussed issues and identified action items related to an overall vision for and proposed models for a shared proteomics reagents resource, applications of affinity capture methods in cancer research, quality control and validation of affinity capture reagents, considerations for target selection, and construction of a reagents database. (
  • To be clinically useful, however, these high throughput proteomics technologies must identify low abundance proteins linked to cancer processes, be sufficiently specific and sensitive to support diagnostic monitoring applications, and be reproducible and scalable for clinical use. (
  • A database that is centralized, public, and standards compliant and contains a variety of proteomics data. (
  • A tool used to view spectra from within the Proteomics Identifications Database. (
  • Thermo Scientific Proteome Discover 2.2 software, which is designed for a range of proteomics workflows and supports multiple database search algorithms and advanced acquisition methods provided by Orbitrap mass spectrometers. (
  • The new Pathway Over-representation application helps proteomics researchers detect significant pathways within genes or proteins: Statistical analyses detect pathways that are either over- or under-represented. (
  • RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. (
  • Interaction with redox regulatory protein APEX seems to activate CTAD. (
  • The present study conducts a comprehensive assessment of transcriptional regulatory pathways in humans for seven well-studied transcription factors: MYC, NOTCH1, BCL6, TP53, AR, STAT1, and RELA. (
  • The results of this study show that for the majority of pathway databases, the overlap between experimentally obtained target genes and targets reported in transcriptional regulatory pathway databases is surprisingly small and often is not statistically significant. (
  • Our study opens a debate on validity of using many popular pathway databases to obtain transcriptional regulatory targets. (
  • Agoston V , Csermely P and Pongor S (2005) Multiple weak hits confuse complex systems: a transcriptional regulatory network as an example. (
  • There is evidence, that ciliary proteins are organized in cell/context specific complexes and/or in shared regulatory circuits in cilia of affected tissues. (
  • A modular configuration might be advantageous: it allows signaling proteins to expand their regulatory linkages and may elicit a broader range of control mechanisms either via modular combinations or through modulation of inter-modular linkages. (
  • In many gram-positive bacteria, the expression and interaction of different ArgR-like proteins may imply a complex regulatory network in response to environmental stimuli. (
  • Another extensively studied type of interactome is the protein-DNA interactome, also called a gene-regulatory network , a network formed by transcription factors, chromatin regulatory proteins, and their target genes. (
  • Similarly, gene regulatory networks overlap substantially with protein interaction networks and signaling networks. (
  • Finally, we discuss the possible role of oligomeric transitions in the regulation of protein activity and compile a set of experimental examples with such regulatory mechanisms. (
  • However such methods are far less tractable for holistic cellular models, which are instead represented at the level of network topology. (
  • PI3K is a large duel lipid and protein kinase that catalyzes phosphorylation of the 3-hydroxyl position of phosphatidylinositides (PIs) and plays a crucial role in the cellular signaling network. (
  • The proteasome is involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. (
  • Almost all cellular RNAs interact with RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs). (
  • Pathway analysis indicated alterations in critical cellular processes related to cell communication and signal transduction, immune response, lipid transport, and metabolism. (
  • To study cellular events underlying oriented growth and morphogenesis, we developed imaging and segmentation methods that allow us to track every cell in the wing and analysis methods to quantify contributions of cell division, cell rearrangement and cell deformation to tissue size and shape changes [1-4]. (
  • These methods have revealed the cellular basis of larval wing growth and pupal wing morphogenesis, and allow us to analyse the effects of mechanical and genetic perturbations in unprecedented detail (Dye et al. (
  • In this work, we provide evidence that astrovirus RNA replication and virus assembly occur in contact with cell membranes potentially derived from multiple cell organelles and show that membrane-associated cellular proteins involved in lipid metabolism are required for efficient viral replication. (
  • These involve activation of several processes at cellular level including epithelial-mesenchymal transition (EMT), motility, adhesion and invasiveness that are regulated by activation of oncogenes, proteases and other tumor-microenvironment components and inactivation of tumor suppressor proteins and apoptosis-mediating factors [ 4 - 7 ]. (
  • The translated proteins are both RLKs with extra-cellular leucine rich repeats (LRR). (
  • The novel Krüppel-like zinc finger protein Gli-similar 2 (Glis2), one member of the transcription factors, is involved in controlling the flow of genetic information and the modulation of diverse cellular activities. (
  • The sequence conservation of functionally important residues across protein interfaces allows the prediction of disease‐associated mutations. (
  • Structure-Activity Relationships in Peptide-Antibody Complexes: Implications for Epitope Prediction and Development of Synthetic Peptide Vaccines by Shu-wen Chen, Marc Van Regenmortel, Jean-Luc Pellequer (953-964) . (
  • A conceptual map of PPI prediction methods. (
  • Aloy P and Russell RB (2003) InterPreTS: protein interaction prediction through tertiary structure. (
  • Comprehensive subcellular location analysis for all E. coli proteins, created using the publicly available prediction algorithms together with experimental data and in-house manual curation. (
  • However, there are few freely available databases integrating both the in vivo and the in vitro skin sensitization assays for development of AOP-based skin sensitization prediction models. (
  • To facilitate the development of AOP-based prediction models, a skin sensitization database named SkinSensDB has been constructed by curating data from published AOP-related assays. (
  • Advanced Chemistry Development -- Developers of chemical property prediction software and spectroscopic databases. (
  • Aggrescan3D - web server for prediction of aggregation propensity in protein structures and rational design of protein solubility. (
  • InterPreTS: protein Interaction Prediction through Tertiary Structure. (
  • Such prediction relies on the well-established paradigms that similar protein sequences imply similar three-dimensional structures. (
  • The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. (
  • However, a significant number of the predicted ORFs do show similarities to functionally classified genes with defined roles in the complex network of metabolic pathways. (
  • This work shows that a crucial factor in predicting and rationalizing protein-protein interfaces can be inferred by assessing the extent of intramolecular desolvation of backbone hydrogen bonds in monomeric structures. (
  • Our statistical analysis of native structures shows that, in the majority of soluble proteins, most backbone hydrogen bonds are thoroughly wrapped intramolecularly by nonpolar groups except for a few ones. (
  • In view of this, we expect that most native structures of soluble proteins in their monomeric form would have most of their hydrogen bonds thoroughly dehydrated to warrant their overall stability. (
  • The Enzyme Structures Database contains all enzymes of known 3D structure, deposited in the Protein Data Bank (PDB) and categorized according to the E.C. numbering system. (
  • PoreLogo is an automated tool for visualizing the sequence and residue conservation of pore-lining residues in transmembrane protein structures. (
  • Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. (
  • According to the traditional sequence-to-structure-to-function paradigm, active proteins have well-defined three-dimensional structures under physiological conditions. (
  • This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. (
  • The availability of the neutron diffractometer led to the determination of a number of protein structures. (
  • Glycans are extremely complex and diverse in their structures and thus it has been necessary to develop a wide range of experimental techniques and instrumentation for their detection and analysis. (
  • Our approach to modular decomposition relies on a representation of protein structures as residue-interacting networks, and removal of the most central residue contacts, which are assumed to be crucial for allosteric communications. (
  • The modular decomposition of 100 multi-domain protein structures indicates that modules constitute the building blocks of domains. (
  • Recently, we introduced a model based on a network representation of protein structures. (
  • The database is available online and completely searchable by keywords or chemical structures. (
  • We generated a model of TMC1 based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway. (
  • Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75(NTR)) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. (
  • ModView, visualization of multiple protein sequences and structures. (
  • The structures identify the filament-forming interfaces, which encode the dsRNA binding cooperativity and length specificity of MDA5. (
  • Fibrous proteins display different sequences and structures that have been used for various applications in biomedical fields such as biosensors, nanomedicine, tissue regeneration, and drug delivery. (
  • The Catalytic Site Atlas is a database documenting enzyme active sites and the catalytic residues in enzymes of known 3D structure. (
  • The active site is in between the trimer-trimer interface and has 3 monomers: A, A′, B. There are three histidine residues that form the metal-binding site in the substrate binding pocket: His 23,48 and 50. (
  • Hotspot residues provide the largest contribution to protein-protein binding energy. (
  • The positions of the residues in the complex suggest that the mutant residues affect the positioning of the cleaved phosphodiester bond in the active site without disruption of the ligation step. (
  • Transgenic expression of the native APB-containing AtbHLH protein, PIF4, in a pif4 null mutant, rescued the photoresponse defect in this mutant, whereas mutated PIF4 constructs with site-directed substitutions in conserved APB residues did not. (
  • Promptly identify a smaller set of residues at a protein interface that are suitable starting points for small-molecule style. (
  • We show that protein domains consist of modules interconnected by residues that mediate signaling through the shortest pathways. (
  • The inter-modular boundaries contain most of the residues centrally conserved in the protein fold, which may be crucial for information transfer between amino acids. (
  • 11 ] considered the residues local environments and designed the conjoint triad method. (
  • Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. (
  • Our integration of RBD discovery by CAPRI with FA- and UV-mediated interactome capture provides the basis for a more complete understanding of the metazoan RNA-protein interaction network. (
  • These data sets, and many others, have increased the amount of available protein interaction data hugely over the past 10 years, but currently, they are all collated into different protein interaction databases ( Arabidopsis Interactome Mapping Consortium, 2011 ). (
  • The aim of our study was to assess the differential gene expression of Parkinson protein 7 (PARK7) interactome in malignant pleural mesothelioma (MPM) using data mining techniques to identify novel candidate genes that may play a role in the pathogenicity of MPM. (
  • We constructed the PARK7 interactome using the ConsensusPathDB database. (
  • We then interrogated the Oncomine Cancer Microarray database using the Gordon Mesothelioma Study, for differential gene expression of the PARK7 interactome. (
  • Finally, Gene Ontology annotation enrichment analysis revealed significant roles of the PARK7 interactome in NuRD, CHD, and SWI/SNF protein complexes. (
  • Finally, we identified that PARK7 interactome is involved in novel pathways pertinent in MPM disease. (
  • Most commonly, interactome refers to protein-protein interaction (PPI) network (PIN) or subsets thereof. (
  • Estimates of the yeast protein interactome. (
  • Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. (
  • Our study compares the RBPs captured by formaldehyde (FA) and ultraviolet (UV) crosslinking at a high-throughput level, and shows that FA crosslinking can retrieve not only direct RNA binders but also the secondary layer of RNA-interacting proteins. (
  • Recently, however, experimental methods for high-throughput and high-resolution identification of RBP binding sites have been developed. (
  • PA is a web server built to predict protein properties, such as general function, in a high-throughput fashion. (
  • For instance, high throughput machine and deep learning is a rational drug design method that benefits the discovery and development of drugs targeting specific proteins. (
  • We discuss the main promises and pitfalls of different methods and present several approaches to verify and validate the diverse experimental data produced by high-throughput techniques. (
  • Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. (
  • In recent years, high-throughput techniques have produced large networks of interacting molecules, which are represented as nodes linked by edges in complex graphs. (
  • BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution. (
  • this revealed a link between arginine biosynthesis and a still-unknown CO 2 -dependent metabolic pathway. (
  • Gene ontology and protein-protein interaction network analysis showed that groups of proteins with roles in fatty acid synthesis and ATP biosynthesis were highly enriched in the fractions of this population in infected cells. (
  • This phenotype was used in a positive screening to select spontaneous mutants deregulated in the arginine biosynthesis pathway. (
  • These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. (
  • One very interesting hypothesis has been generated regarding the regulation of yeast glycolysis by a protein found to interact with seven glycolytic enzymes. (
  • Conventional methods of inhibitor design mostly target RNA-processing enzymes and cannot be generalized to the majority of RNA-binding proteins (RBPs). (
  • Sequential enzymes in biosynthetic pathways are organized in metabolons. (
  • These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. (
  • For instance, protein interactomes contain many enzymes which in turn form biochemical networks. (
  • Many soluble and membrane proteins form homooligomeric complexes in a cell which are responsible for the diversity and specificity of many pathways, may mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell adhesion processes. (
  • This suggests that each PKMT methylates multiple proteins, however till now only one or two substrates have been identified for several of these enzymes. (
  • Many proteins are enzymes that catalyze the chemical reactions in metabolism. (
  • Plants have evolved intracellular immune receptors to detect pathogen proteins known as effectors. (
  • On the intracellular side, these transmembrane proteins are connected to the actin cytoskeleton via protein complexes including zonula occludens (ZO) proteins. (
  • The intracellular orientation of these complexes is organized in global patterns that change dynamically during growth and morphogenesis [7, 8]. (
  • Within the crowded intracellular environment, proteins are constantly coming into physical contact. (
  • Disease‐associated genes tend to be clustered together in protein-protein interaction networks. (
  • These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. (
  • The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. (
  • Date SV and Chen G (2007) Interaction networks of proteins. (
  • ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. (
  • At the same time, PINA allows users to either edit the network generated from the public data, or combine these with uploaded private data to build more complete protein-protein interaction networks. (
  • Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. (
  • 2014) ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks. (
  • UPLC/ESI-Q-TOF/MS combined with pattern recognition approaches including PCA, and PLS-DA were integrated to get differentiating metabolites for the pathways and clarify mechanisms of disease, highlight insights into drug discovery. (
  • Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. (
  • These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. (
  • Although it has traditionally been viewed as simple deposition of lipids within the vessel wall, it is now assumed that atherosclerosis is a multifactorial disease that involves several genes and proteins, activated during its genesis, progress, and phenotypic manifestation. (
  • In contrast, mitochondria are not connected to vesicular trafficking pathways, and many lipids of the inner and outer mitochondrial membranes (IMM and OMM) cannot be synthesized within mitochondria but are imported by unclear mechanisms. (
  • or anabolic - the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). (
  • Given that MYC is involved in the transcriptional regulation of approximately 15% of all genes [ 8 ], one cannot argue that the majority of pathway databases that contain less than thirty putative transcriptional targets of MYC are even close to complete. (
  • Different evolution-based methods, such as conservation and coordinated mutations analyses, have been examined to address this issue. (
  • Disease‐associated mutations often affect protein-protein binding affinities that can be measured with high accuracy in vitro using purified proteins by a variety of biophysical techniques. (
  • The crystal structure of the Pikp-HMA/AVR-PikD complex enabled design of mutations to alter protein interaction in yeast and in vitro, and perturb effector-mediated response both in a rice cultivar containing Pikp and upon expression of AVR-PikD and Pikp in the model plant Nicotiana benthamiana . (
  • 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. (
  • The predicted naproxen binding sites were tested using the Y148A, R152A, R355A, and R361A proteins carrying single-point mutations. (
  • The throughput of these techniques is limited due to the heterogeneity in peptide-ribonucleotide conjugates and difficulty of identifying the conjugated peptide tandem MS spectra by standard database search engines. (
  • Current Protein and Peptide Science 13 (1): 19-33. (
  • The data contained within is primarily protein and peptide IDs, MS mass spectra, and any related metadata. (
  • The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy. (
  • Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. (
  • Among these, an interesting sequence-based approach has been proposed by Ranganathan and coworkers [ 14 , 15 ] for estimating the thermodynamic coupling between amino acids in several examples of protein families. (
  • More specifically, the PSSMs are generated using the information of protein amino acids sequence. (
  • Recently, the methods based on the sequence information of protein amino acids for detecting PPI have been proposed [ 22 - 24 ]. (
  • The complex environment of a living cell contains many molecules interacting in a variety of ways. (
  • Currently, protein-protein interaction surfaces are mostly considered undruggable by small molecules. (
  • Nucleotide-binding, leucine-rich repeat receptors (or NLRs for short) are plant proteins that survey the inside of plant cells looking for these telltale molecules. (
  • Its chief aim is to help experimentalists, planning to solve a specific protein structure, to identify small molecules that might form a complex with the protein. (
  • The ability to modulate protein function using exogenous small molecules is a longstanding goal in chemical biology. (
  • In parallel to these efforts I carried out studies aimed at inhibition of protein function, as exemplified by my project that uses small molecules to disrupt a protein-RNA interaction. (
  • The comparison of docking molecules for proteins, other drug-like molecules, or even fragments from the original molecule enables a pool of prominent candidates to be calculated with listed values. (
  • Chemical sensitizers, which may be detergents, preservatives, or fragrances in household and personal care products or active ingredients, impurities from synthetic process and industrial materials in the pharmaceutical products, act as haptens binding to protein molecules. (
  • The Common Fund Program - Accelerating Translation of Glycoscience: Integration and Accessibility - aims to develop accessible and affordable new tools and technologies for studying carbohydrates that will allow biomedical researchers to significantly advance our understanding of the roles of these complex molecules in health and disease. (
  • In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. (
  • We have simulated with reasonable fidelity the measurable static and dynamic properties of the several different proteins surrounded by thousands of water molecules. (
  • Satellite nodes can be switched on to show the associated Uniprot protein sequence ids, PDB codes, or E.C. enzyme classification numbers. (
  • It uses both sequence- and structure-based methods to try to provide clues as the the protein's likely or possible function. (
  • Protein C, the zymogen of APC, is synthesized as a single chain precursor containing an amino-terminal leader sequence followed by a propeptide, which are cleaved upon secretion. (
  • Since no sequence information is transmitted over the Internet, PathwayVoyager is an ideal solution for pathway mapping and reconstruction of confidential DNA sequence data. (
  • The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. (
  • 25 ] used only protein sequence information to predict PPI, in which a kind of method called PCA-EELM (Principal Component Analysis-Ensemble Extreme Learning Machine) is designed. (
  • Second we are interested in predicting protein structure from sequence without regard for the process of folding. (
  • A system designed to map protein sequences with protein IDs. (
  • A tool used to generate custom databases of FASTA sequences. (
  • We downloaded the sequences flanking all human genes from internet resources and identified repetitive elements by cross-matching sequences against RepeatMasker database. (
  • An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. (
  • A fundamental discovery was her work to define key biophysical mechanisms in protein complex assembly, showing that protein complexes assemble via distinct, ordered pathways. (
  • The Cofactor database presents information and catalytic mechanisms, compiled from the scientific literature, relating to organic enzyme cofactors. (
  • MACiE - M echanism, A nnotation and C lassification i n E nzymes - is a database of fully annotated enzyme reaction mechanisms. (
  • Further studies on the identified proteins could provide crucial information to understand possible mechanisms of toxicity of single xenobiotics or mixtures of them in marine ecosystems. (
  • This emphasizes the importance of constructing tissue-specific interactomes and their constitutive pathways for understanding mechanisms that differentiate cell types and make them uniquely susceptible to tissue-specific disorders. (
  • We particularly focus on homooligomer evolution and describe the mechanisms to develop new specificities through the formation of different homooligomeric complexes. (
  • Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. (
  • In addition, using experimentally derived NMR restraints, we used the program HADDOCK to calculate a low-resolution model of the complex formed in solution by these two PAS domains, and confirm the validity of this model using site-directed spin labeling to obtain long-range distance information in solution. (
  • Then the lists of experimentally obtained direct targets are compared with relevant lists of transcriptional targets from 10 commonly used pathway databases. (
  • We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer -related or damaging SNPs. (
  • The database is an extension of the MACiE database ( see above ) and is the result of a collaborative project among three institutes: the Magnetic Resonance Center (University of Florence), the European Bioinformatics Institute and the Unilever Center (University of Cambridge). (
  • The goal for the Biostatistics and Bioinformatics for Basic Scientists course is to provide an introduction to statistics and informatics methods for the analysis of data generated in biomedical research. (
  • Oligonucleotide DNA microarrays, for example, have depended on bioinformatics for initial development and ongoing advances in measurement tools and analysis methods. (
  • With each new platform or modification, researchers depend on bioinformatics for probe development, analysis methods and visualization software. (
  • Similarly, Pathway Tools utilizes dedicated server and database backbones to realize a sophisticated environment. (
  • This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). (
  • As soon as a new tool-related publication is published in JIB, the tool is posted to and can afterwards be easily transferred to, a large information repository of software tools, databases and services for bioinformatics and the life sciences. (
  • We shall demonstrate the use of a simple web interface to perform common bioinformatics tasks and show the power of parallel computing on grid to reduce the running time of these tasks. (
  • Teichmann's research investigates gene expression and protein complex assembly using both wet laboratory and computational biology techniques. (
  • Two different ways of studying each pathway are provided: querying it by up- or down-regulating specific components, or importing gene expression data and phenotype information (lifespan extension/reduction) and inferring the effects on the pathway. (
  • proposals which define interfaces and services in support of array based gene expression data collection, management, retrieval, and analysis. (
  • Mining gene expression databases for association rules. (
  • Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. (
  • The only exception is MetaCore pathway database which yields statistically significant intersection with experimental results in 84% cases. (
  • Experimental methods point to identify hotspots and quantify binding energy. (
  • Our group has developed Experimental Information and Data Repository ( and the MicrobesOnline database to provide this functionality. (
  • Other remote software solutions like DAVID [ 6 ] integrate various databases and experimental results to allow for extensive query-based data mining on given gene lists. (
  • A) Expression of promoter-GFP fusion (Experimental Methods) in L2, L4 and early adult. (
  • Analysis of several protein families showed an agreement between our results and experimental data, illustrating the importance of protein topology in network communications. (
  • Furthermore, as more and more genomes are sequenced, only a fraction of proteins will have additional data to complement any experimental HTP study. (
  • Further, in many experimental methods, the confidence of observations is evaluated for that specific technique - they are seldom generalizable. (
  • We provide experimental evidence and demonstrate that CAPE induced disruption of mortalin-p53 complexes led to nuclear translocation and activation of p53 resulting in growth arrest in cancer cells. (
  • In this review we describe different experimental techniques of protein interaction identification together with various databases which attempt to classify the large array of experimental data. (
  • One of these is the hypoxia response pathway, which allows eukaryotic cells to respond to low oxygen tension via the formation of a heterodimeric complex between ARNT and another bHLH-PAS protein, the hypoxia-inducible factor alpha (HIF-alpha). (
  • human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (
  • For one protein trafficking pathway in eukaryotic cells, however, the determinative protein self-assembly occurs not in the cytoplasm but within the lumen of the secretory pathway itself. (
  • It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms (Human, Arabidopsis, Fruit Fly, Worm, Mouse,Rat & Yeast). (
  • For example, deletion of MNN10 , HOC1 , and MNN11 , genes all involved in protein transport and membrane-related processes, had a negative effect on many of the yeast strains with an extra chromosome. (
  • Here we investigate the involvement of the yeast anaphase promoting complex (APC) in longevity. (
  • looked for a proteinaceous link between the ER and mitochondria and, using combinations of synthetic biology and classical yeast genetics, found a protein complex that tethers the two organelles. (
  • The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. (
  • The protein encoded by GmRLK18-1 ( Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean (Glycine max L. Merr. (
  • Two loci, Rhg4 on chromosome 8 (linkage group (Lg) A2) and Rhg1/Rfs2 on chromosome 18 (Lg G), contain genes that encode receptor like kinase (RLK) proteins within the RPK gene family implicated in resistance. (
  • Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. (
  • Through YeastMine, questions such as "What proportion of plasma membrane proteins are essential ? (
  • Popular commercial products, such as MetaCore [ 6 ], Ingenuity Pathway Analysis, Pathway Studio and Biobase Knowledge Library (TRANSPATH and TRANSFAC) are often based on literature curation (e.g. (
  • Mass spectrometers, for example, help identify proteins by matching the mass/charge of their constitutive peptide's fragments against a database. (
  • Evidence for this mechanism includes in vitro experiments showing that some proteins released via constitutive exocytosis remain soluble under TGN-like conditions that promote DCG protein aggregation ( 10 ). (
  • The Metal MACiE database annotates both the properties and functions of the metal ions involved in enzyme catalytic reactions. (
  • Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. (
  • The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. (
  • This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. (
  • Lysine methylation is an emerging post-translation modification and it has been identified on several histone and non-histone proteins, where it plays crucial roles in cell development and many diseases. (
  • SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. (
  • The database is represented by a web-based browser and a multitude of different analyses are possible. (
  • Extensive analyses of transcriptome have been carried out in chickpea, which is the third most important legume valued as a source of dietary protein and micronutrients. (
  • Galaxy's user-friendly, web-based interface makes it possible for anyone, regardless of their informatics expertise, to create, run, and share large-scale robust and reproducible analyses. (
  • Her databases and computational analysis methods have had a broad and deep impact on the community. (
  • Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. (
  • Current network analysis packages tend to be standalone desktop tools which rely on local resources and whose operations are not easily integrated with other software and databases. (
  • In addition, PINT allows developers to incorporate data visualization and analysis tools, such as PSEA-Quant and Reactome pathway analysis, for data set enrichment analysis. (
  • To address this need, we have developed the CLIPZ database and analysis environment. (
  • Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. (
  • The analysis of protein-protein interfaces is crucial to quantify protein complex stability. (
  • c) analysis by gene sets and pathway. (
  • Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. (
  • thus quantitative analysis for complex proteomes has increasingly become a critical way to investigate the mechanism of disease. (
  • A great resource for meta-analysis *[ dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq. (
  • We further introduced seven publicly available RNA methylation-related databases, and some important publicly available RNA-methylation-related Web servers and software for RNA methylation site identification, differential analysis and so on. (
  • To further characterize the role of these repetitive elements in gene regulation, programs for pathway analysis were used to analyze genes from various repeat groups. (
  • 2012) Genomic analysis of DNA-binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. (
  • Western analysis suggested homo-dimers could form after protein extraction from roots. (
  • Systematic analysis of protein turnover in primary cells. (
  • The data science team themselves are highly skilled in the analysis and interpretation of omics and screening data, advanced data analytics and quantitative methods. (
  • Information in the most popular publicly available pathway databases, such as BioCarta, KEGG [ 4 ], WikiPathways [ 5 ], Cell Signaling Technology pathways is usually either curated by efforts of a particular academic group (e.g. (
  • Currently, there are more than 10 publicly available Arabidopsis ( Arabidopsis thaliana ) protein interaction databases. (
  • Pathway Commons is a collection of publicly available pathway information from multiple organisms. (
  • We propose a new strategy that assigns genes to hierarchical categories (BINs) modelled on the ontology provided by the KEGG database [7]. (
  • KEGG is a pathway-orientated database, which integrates the genes of many species. (
  • The Kyoto Encyclopedia of Genes and Genomes (KEGG) represents a database consisting of known genes and their respective biochemical functionalities. (
  • Presented here is a new software solution that utilizes the KEGG online database for pathway mapping of partial and whole prokaryotic genomes. (
  • PathwayVoyager retrieves user-defined subsets of the KEGG database and stores the data as local, blast-formatted databases. (
  • EC classification), these genes can be marked in corresponding KEGG pathways. (
  • In addition to this web-browser based approach, the KEGG database can also be accessed directly via an application programming interface (API) and the underlying databases can be downloaded for local uses. (
  • PathFinder [ 7 ] and BioMiner [ 8 ] use a different approach in that they utilize some of the data the KEGG database provides and then approach pathway reconstruction using software specific algorithms. (
  • PoreWalker is a fully automated method for detecting and characterizing transmembrane protein channels from their 3D structure. (
  • Tight junction complexes are formed by transmembrane spanning proteins, including claudins, occludin and junctional adhesion molecule, which link neighbouring cells. (
  • The transmembrane channel-like 1 (TMC1) protein localizes to the site of the MET channel, interacts with the tip-link responsible for mechanical gating, and genetic alterations in TMC1 alter MET channel properties and cause deafness, supporting the hypothesis that TMC1 forms the MET channel. (
  • Our mTMC1 models establish the presence of 10 transmembrane (TM) helices, suggest that the TMC proteins are dimers and reveal that the conserved Ca 2+ binding site found in TMEM16 proteins is not conserved in TMC. (
  • A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteins. (
  • You may read the explanation of the method and the full data available from ConSurf . (
  • Integration of different data sets into a protein-protein network. (
  • Accuracy can be increased by considering only the strict intersection of the data sets where a positive PPI (protein-protein interaction) exists in each data set. (
  • Weighted integration counts only the PPIs in each data set considered to be the most reliable through the consultation of an outside gold standard database. (
  • Both the interface and the underlying data pipeline leverage extensively ChemAxon technologies for name to structure conversion, as well as compound standardisation, registration and searching. (
  • Felsenstein J (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. (
  • PDBsum is a pictorial database providing an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). (
  • The requirements for these studies included protein crystals with relatively small unit cells, because of the diffraction data resolution requirements of the linear detector, and extremely large crystals (several millimeters in each dimension), because of the weak flux of the neutron beam (2). (
  • and mainly focus on the metagenomics to discuss current data, method, and opportunity for personalized medicine. (
  • This data file format has the following advantages: (1) Independent of any particular database schema. (
  • The ConsensusPathDB web interface allows users to take advantage of these integrated interaction and pathway data in different contexts. (
  • To facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of ConsensusPathDB using the Cytoscape.js library. (
  • We describe the database schema and the methods used for data integration. (
  • Although significant progress has been made in the standardization of these data types, there is still significant incongruence from one spectral database to another. (
  • 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. (
  • 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. (
  • In addition to non-trivial correlations between these features (that is, co-expression need not imply interaction), these data are not complete for all proteins. (
  • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. (
  • The BMEG data model is instantiated in a scalable graph database optimized for storing and querying graphs containing terabytes of vertices and edges distributed across a multi-machine cluster. (
  • Database providers can share their pathway data via a common repository and avoid duplication of effort and reduce software development costs. (
  • The data proposes that CAPE-γCD complex is a potent anti-cancer and anti-metastasis reagent. (
  • and compatibility of data generated with integration into existing databases. (
  • It is designed to fully utilize high-fidelity Orbitrap data for the accurate identification of compounds in the most complex matrices. (
  • The new Thermo Scientific Xcalibur 4.1 software, an easy-to-use, flexible and efficient solution that enables simple method setup, data acquisition, processing and reporting through an intuitive interface. (
  • The Thermo Scientific FreeStyle 1.3 software, which now features improved usability and offers elemental composition using MS/MS. It is a flexible data visualization solution for information rendering, rapid method development and data quality assessment. (
  • You will be part of a highly motivated, multi-disciplinary team all driven by a passion to improve decision making in Drug Discovery by leveraging advanced data science methods. (
  • GAD Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies). (
  • DDX54, a member of the DEAD-box RNA helicase protein family, has been identified as a hormone-dependent interacting protein of estrogen receptors (ERs) ( 12 ) and CAR-binding protein ( 13 ). (
  • This is only one of the over 40 distinct protein domains known to contact RNA. (
  • Proteins in both pathways localize to adherens junctions and form distinct asymmetric intracellularly polarized complexes that couple the polarity of adjacent cells. (
  • The DUF23 domain is found in 61 predicted proteins in C. elegans, which can be divided into three distinct phylogenetic clades. (
  • The annotation and distribution of distinct classes of repetitive elements associated with individual gene were then used to construct a gene-based repetitive element database (GBRED). (
  • Second, Aplysia bag cells can sort different subsets of DCG proteins into distinct granules, suggesting that aggregation can be finely regulated and that different aggregates have different properties in vivo ( 20 ). (
  • Di Paola L , Paci P , Santoni D , De Ruvo M and Giuliani A (2012) Proteins as sponges: a statistical journey along protein structure organization principles. (
  • Implements a robust statistical framework for the interpretation of protein lists in the context of a global PPI network. (
  • Approaches to reconstruction of haplotypes by genotype inference can be divided into statistical methods and non-statistical methods. (
  • It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. (
  • To facilitate the exploitation of the metabolic model, we provide a web interface allowing online predictions and visualization of results on metabolic maps. (
  • XdomView: protein domain and exon position visualization. (
  • However, proteins which interact with polyA+ RNA indirectly have not been probed on a systematic level until now. (
  • Dandekar T , Snel B , Huynen M and Bork P (1998) Conservation of gene order: a fingerprint of proteins that physically interact. (
  • Influencing these signal transduction pathways holds great potential for pharmaceutical research. (
  • Specific examples of this work include the automatic modeling of antibody variable domains, the general modeling of homologous proteins and studies of DNA base-pair mismatches. (
  • The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). (
  • Although the hydrophobicity of buried positions is a major evolutionary constraint for the stable maintenance of a fold within a superfamily, it is not the only driving force at interfaces because these are usually made of heterogeneous physicochemical textures. (
  • Protein C shares homologies with other vitamin K-dependent coagulation proteins as a result of a common evolutionary pathway. (
  • These similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention is likely due to their efficacy. (
  • Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. (
  • cDNA array performed on the control and CAPE-treated breast cancer cells revealed activation of DNA damage signaling involving upregulation of GADD45α and p53 tumor suppressor proteins. (
  • Of note, we found that whereas CAPE was unstable in the culture medium (as it gets degraded into caffeic acid by secreted esterases), its complex with gamma cyclodextrin (γCD) showed high efficacy in anti-tumor and anti-metastasis assays in vitro and in vivo (when administered through either intraperitoneal or oral route). (
  • It is a complex multi-step phenomenon and involves interplay of several factors that enable cancer cells to acquire invasiveness and intravasate into circulatory system, survive in the blood or lymph circulation, form microvasculature and extravasate to form tumor mass at distant organs [ 1 - 3 ]. (
  • Mutant proteins were tested for the ability to mediate integration in vivo and for in vitro DNA-binding, cleavage, and ligation activities. (
  • Proteins are the most versatile and important macromolecules in life. (
  • One hundred and eleven spots showed a significant increase or decrease in protein abundance in the two-dimensional electrophoresis maps from the groups exposed to pollutants. (
  • In addition to a conventional Z score, the algorithm calculates a D score that takes into account the uniqueness, reproducibility, and abundance of the interacting protein. (
  • For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. (
  • One of the representative methods of label-free quantification is Normalized Spectral Abundance Factor (NSAF) which was firstly proposed by Florens et al. (
  • 10 ] uses a modified spectral counting method which utilizes machine learning technique to arrive at protein abundance values with improved accuracy over traditional spectral counting techniques [ 11 ]. (
  • I mutated a pair of tryptophans at the dimer interface to glycine in order to disrupt the dimerization of ChxR. (
  • Moreover, recent studies have led to a greater awareness that transitions between different oligomeric states may regulate protein activity and provide the switch between different pathways. (
  • Cambridge Healthtech Institute & Bio-IT World Announce Upcoming Short Course: Identification of Druggable Sites for Protein-Protein Interaction Targets June 8, 2011 (6:00 - 9:00 p.m. (
  • To obtain this fundamental information well-defined starting material, optimal fractionation methods and adequate identification techniques are essential. (
  • In this chapter, we will review the theoretical concepts behind different protein-protein docking algorithms, highlighting their strengths as well as their limitations and pointing to important case studies for each method. (
  • Biobase Knowledge Library) and/or complex algorithms for mining biomedical literature (e.g. (
  • Moreover, the existing software has some shortcomings including the requirement for significant manual labor when working with huge lists of SNPs and that algorithms work only for SNPs present in databases such as dbSNP. (
  • A computational perspective on the current state of the methods and challenges in cancer drug discovery looking for high-quality research related to interdisciplinary approaches to exploiting the power of drug discovery by applying new algorithms, tools and databases. (
  • DockVision Docking package which includes Monte Carlo, Genetic Algorithm, and database screening docking algorithms. (
  • i ) Can we identify backbone hydrogen bonds in soluble proteins that are poorly wrapped, i.e., that are poorly dehydrated? (
  • In vivo, sorting would result if aggregated and soluble proteins exit the TGN in different carriers. (
  • NF-κB is a heterodimer protein that consists of two subunits, p65 (RelA) and p50 which are required for activation and nuclear translocation of NF-κB. (
  • NP covers the eight single-stranded segments of the genomic RNA and assembles with the three polymerase subunits in a ribonucleoprotein complex (RNP) controlling viral transcription and replication ( 1 ). (