Tag: protein

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synth ...

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all ...

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More in ...

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

mzML was formed to amalgamate two formats for encoding raw spectrometer data; mzData developed by the PSI, and, mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. The PSI, with full participation by the ISB, develope ...

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.

The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored w ...

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of geneti ...

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic ...

The Protein Quaternary Structure file server (PDBePISA) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank (PDB) that were determined by X-ray crystallogr ...

FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede th ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is know ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

BLAT is a multiple algorithms developed for the analysis and comparison of biological sequences such as DNA, RNA and proteins.

InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as si ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.

PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organis ...

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises a ...

This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for clas ...

PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.

The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any struct ...

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lin ...

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions ...

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are fi ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete ...

CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test. It is used for the ontology based application for statistical analysis on COG db.

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

MIAPE attempts to define the minimum set of information about whole proteomics experiments that would be required by a public repository.

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. ...

The PSI-MI interchange format and accompanying controlled vocabularies was originally designed by a consortium of molecular interaction data providers from both academia and industry, including BIND, DIP, IntAct, MINT, MIPS, GlaxoSmithKline, CellZome ...

The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.

The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The anti ...

IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (Ig ...

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication ...

PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

A database of exosomes, membrane vesicles of endocytic origin released by diverse cell types.

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

An exchange format for reporting experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, ...

The MIASE Guidelines, initiated by the BioModels.net effort, are a community effort to identify the Minimal Information About a Simulation Experiment, necessary to enable the reproducible simulation experiments. Consequently, the MIASE Guidelines lis ...

The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs ...

MIMIx is a community guideline advising the user on how to fully describe a molecular interaction experiment and which information it is important to capture. The document is designed as a compromise between the necessary depth of information to desc ...

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

NCBI Virus is a community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories.

BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.

The PSI-MS Controlled Vocabulary is developed in common with the PSI-Proteomics Informatics group. It consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identificati ...

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.

The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.

MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database ...

Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Databas ...

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family. A fingerprint is a group of conserved motifs used to characterize a protein family. Usually, the motifs do not overlap, though they ma ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-co ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene s ...

The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated int ...

MycoCosm provides data access, visualization, and analysis tools for comparative genomics of fungi. MycoCosm enables users to navigate across sequenced fungal genomes, and to conduct comparative and genome-centric analyses of fungi and community anno ...

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in ...

PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 con ...

BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model ...

STRENDA stands for “Standards for Reporting Enzymology Data”. For researchers it is essential to be able to compare, evaluate, interpret and reproduce experimental research results published in the literature and databases. Thus, for enzyme research, ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned ...

The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...

The Structural Biology Data Grid (SBGrid-DG) community-driven repository to preserve primary experimental datasets that support scientific publications. The SBGrid Data Bank is an open source research data management system enabling Structural Biolog ...

The MITAB27 format is an extension of the PSI-MI 2.5 (1) and 2.6 standard. It has been derived from the tabular format provided by BioGrid. MITAB27 only describes binary interactions, with one pair of interactors per row.

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made ...

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provid ...

ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.

The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.

PDB-REDO is a databank of optimised (re-refined, rebuilt and validated) Protein Data Bank entries. It covers nearly all structure models derived from X-ray and electron diffraction that have deposited experimental data. Entries can be accessed by the ...

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is appli ...

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of ge ...

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

TargetMine integrates many types of data for human, rat and mouse. Flexible queries, export of results and data analysis are available.

PDBx/mmCIF is a dictionary of data archiving macromolecule crystallographic experiments and their results.

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

MIAPAR is intended to be used as a guideline for experimentalists who wish to unambiguously describe protein affinity reagents and their protein targets (including but not limited to Ab/Ag interactions). It specifies the minimum amount of information ...

BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships str ...

The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Ag ...

The goal of the Gene Wiki is to apply community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated w ...

ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they mo ...

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome ...

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of d ...

GelML is a data exchange format for describing the results of gel electrophoresis experiments. GelML is developed as a HUPO-PSI working group.

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also ...

The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

The HIV-1, human protein interaction data presented here are based on literature reports. This dataset is available in report pages per HIV-1 protein and is also integrated into Entrez Gene report pages for HIV-1 and human proteins.

Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.

The database provides a centralised repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily ( ...

Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.

This module identifies the minimum information required to report the use of a mass spectrometer in a proteomics experiment, sufficient to support both the effective (re-)interpretation and (re-) assessment of the data and the potential reproduction ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

The mzQuantML standard format is intended to store the systematic description of workflows quantifying molecules (principally peptides and proteins) by mass spectrometry. A large number of different software packages are available that produce output ...

The IPD-MHC Database provides a centralised repository for sequences of the Major Histocompatibility Complex (MHC) from a number of different species. Through a number of international collaborations IPD is able to provide the MHC sequences of differ ...

This module identifies the minimum information required to report the use of protein and peptide identification and characterisation software to analyse the data produced by mass spectrometry experiments, sufficient to support both the effective inte ...

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.

This module identifies the minimum information required to report the use of quantification techniques in a proteomics experiment, sufficient to support both the effective interpretation and assessment of the data and the potential recreation of the ...

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musc ...

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textboo ...

Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.

ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, M ...

iProX is a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based ...

The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

Reporting requirements for the evaluation of recombinant protein functionality – MIPFE version 0.1. Please note: We cannot find an up-to-date website for this resource. As such, we have marked it as Uncertain. Please contact us if you have any inform ...

SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about ex ...

Unimod is a community-supported, comprehensive database of protein modifications for mass spectrometry applications. The aim is to provide accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all ...

A large number of different proteomics search engines are available that produce output in a variety of different formats. It is intended that mzIdentML will provide a common format for the export of identification results from any search engine. The ...

PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and ...

SPRINT provides search access to the data bank of protein family fingerprints (PRINTS).

PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic techno ...

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

Human Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations.

HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the ty ...

Drug Target Ontology (DTO) is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The fir ...

This module identifies the minimum information required to report an informatics analysis performed with gel electrophoresis images, in a manner compliant with the aims as laid out in the ‘MIAPE Principles’ document.

KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. This resources provides plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme ...

MIAPE - Column Chromatography (MIAPE-CC) is one module of the Minimal Information About a Proteomics Experiment (MIAPE) documentation system. MIAPE is developed by the Proteomics Standards Initiative of the Human Proteome Organisation (HUPO-PSI). It ...

KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The da ...

The scopes of molecular interactions and protein affinity reagents are largely overlapping but are also partially unique. This fact is reflected in the PSI-PAR CV, which contains the majority of the terms from the PSI-MI CV and an additional ∼200 new ...

The compendium of crop Proteins with Annotated Locations (cropPAL) collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

“MIAPE – Capillary Electrophoresis” (MIAPE-CE) is one module of the Minimal Information About a Proteomics Experiment (MIAPE) documentation system. MIAPE is developed by the Proteomics Standards Initiative of the Human Proteome Organisation (HUPO-PSI ...

CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, pro ...

MitoProteome is a mitochondrial protein sequence database and annotation system. The initial release contains 847 human mitochondrial protein sequences, derived from public sequence databases and mass spectrometric analysis of highly purified human h ...

CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.

Domain mapping of disease mutations (DMDM) is a database in which each disease mutation can be displayed by its gene, protein or domain location.

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repea ...

The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well a ...

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in- ...

LinkProt collects information about protein chains and complexes that form links. LinkProt detects deterministic links (with loops closed by cysteine), and determines likelihood of formation of links in networks of protein chains called MacroLinks. L ...

ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.

The Integrated Interactions Database (IID) is a database of detected and predicted protein-protein interactions (PPIs) in a number of species. It stores networks that are specific to tissues, sub-cellular localizations, diseases, and druggable protei ...

Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utiliz ...

The Proteomics Informatics Working Group is developing standards for describing the results of identification and quantification processes for proteins, peptides, small molecules and protein modifications from mass spectrometry. This working group is ...

fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molec ...

The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information o ...

HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).

GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive liter ...

REFOLDdb is a resource for the optimization of protein refolding, referring to published methods employed in the refolding of recombinant proteins. It stores a collection of published experimental approaches and records for refolding proteins. It con ...

CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biologic ...

Colorectral Cancer Atlas is an web-based resource which integrates genomic and proteomic pertaining to colorectal cancer cell lines and tissues. Data catalogued includes, quantitative and non-quantitative protein expression, sequence variations, cell ...

A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. The Molecular Interactions Working group page can be found at http://www.psidev.i ...

An InterMine interface to data from Phytozome

EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.

Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family class ...

SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural para ...

WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: - Metabolite concentrations, - DNA, RNA and protein expression, - DNA-bound ...

mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin.

HypoxiaDB is a manually-curated non-redundant catalogue of human hypoxia-regulated proteins with a goal of collecting proteins whose expression patterns are altered in hypoxic conditions.

PSIbase is a molecular interaction database based on PSIMAP (PDB, SCOP) that focuses on structural interaction of proteins and their domains. This resource has been marked as Uncertain because its project home can no longer be found. Please get in to ...

AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo s ...

EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...

Relative evolutionary importance of amino acids within a protein sequence.

The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores inform ...

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

The AlloMAPS database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations. In addition to energetics of allosteric sig ...

A public standards-compliant repository for gel-based proteomics data linked to protein identification published in the literature. The repository is continuously extended, putting together a large collection of multi-species reference maps, with tho ...

SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nu ...

The sepCV is a controlled vocabulary for teminology associated with sample preparation and sample processing for proteomics. The sepCV was originally designed to provide terminology for the MIAPE GE reporting guidelines and the gelML data transfer fo ...

The work on PSI-PAR was initiated as part of the ProteomeBinders project and carried out by EMBL-EBI and the PSI-MI work group. The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to faci ...

GlycoProtDB is a glycoprotein database providing information of Asn (N)-glycosylated proteins and their glycosylated site(s), which were constructed by employing a bottom-up strategy using actual glycopeptide sequences identified by LC/MS-based glyco ...

SURFACE is a database containing the results of a large-scale protein annotation and local structural comparison project. The homepage of the resource has not been updated since 2003 (and the maintainer's website since 2010). Until we have confirmati ...

InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interac ...

The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. PLIO represents knowledge about the interaction o ...

The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.

FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes and nuclear receptors, offering both graphical and quantitative data on th ...

BCL2DB is a database designed to integrate data on BCL-2 family members and BH3-only proteins.

A database dedicated to the tyrosine kinase recepter.

Conformation Angles DataBase [ CADB-3.0 ] is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present ...

The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RD ...

Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, on ...

MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.

This mine integrates many types of data for string bean built from the LIS chado database.

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

The Blue Star STING database stores information on the interactions between proteins and other bio macromolecules. Structure descriptors used in the analysis of these interactions are stored in STING DB to aid research primarily into the problems cha ...

The Morphinome Database is repository for proteins regulated by morphine administration.

Vertebrate Secretome Database (VerSeDa) stores information about proteins that are predicted to be secreted through the classical and non-classical mechanisms, for the wide range of vertebrate species deposited at the NCBI, UCSC and ENSEMBL sites.

AlphaFold DB provides open access to 3D protein structure predictions for the human proteome and 20 other model organisms to accelerate scientific research. It is based on AlphaFold AI system developed by DeepMind.

The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast ...

A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.

The HUPO-PSI Protein Separation work group is a collaboration of researchers from academia, industrial partners and software vendors. The group aims to develop reporting requirements that supplement the MIAPE parent document, describing the minimum i ...

The "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu.

The Molecular Connections Cell Line Ontology models primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-mo ...

The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains the seed protein sequence alignments from the Pfam-A (curated families) database; nucleotide sequence alignments derived f ...

With the rapid progress of the HLPP (Human Liver Proteome Project), a massive quantity of liver proteome expression profile data has been generated. To manage the valuable resource effectively and present it for researchers, a web-based database of l ...

BenchSci is a free platform designed to help biomedical research scientists quickly and easily identify validated antibodies from publications. Using various filters including techniques, tissue, cell lines, and more, scientists can find out publishe ...

The glycobiology of Drosophila has been extensively studied in recent years, and much information has accumulated regarding glycan-related genes and proteins in Drosophila. The FlyGlycoDB ontology describes glycogenes of Drosophila and includes mutan ...

This PIR Database File Structure and Format Specification describes the files comprising the PIR-International Protein Sequence Database and the format of each. The format has been enhanced significantly for Release 39.00 to what is referred to as "e ...

"mini Protein Data Bank Format" is a standard. This text was generated automatically. If you work on the project responsible for "mini Protein Data Bank Format" then please consider helping us by claiming this record and updating it appropriately.

>>>!!!<<< Offline, actually no valid URL 2020-09-30 >>>!!!<<< A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the g ...

>>>!!!<<< Offline, actually no valid URL 2020-09-30 >>>!!!<<< The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and ...

PDZscape is a compilation of all existing PDZ-containing proteins on a single platform. It provides a user friendly search interface that enables the database to be queried using the names and external identifiers.

The BcForms represents complexes as a sets of subunits, including their stoichiometries, and a set of interchain/intersubunit crosslinks. Furthermore, BcForms can be combined with BpForms and SMILES descriptions of subunits to calculate properties of ...

XML Schema definition for the UniProtKB XML format.

iSpyBio is an intelligent and unbiased search engine for Life scientists. It ranks reagents by the number of data such as publications, reviews, characterization images and tested applications. It displays over 500,000 reagents such as antibodies, pr ...

The UniProt core is an OWL ontology that describes the predicates, classes and concepts used to model the UniProt data in RDF.

The glycobiology of Drosophila has been extensively studied in recent years, and much information has accumulated regarding glycan-related genes and proteins in Drosophila. As a database for glycan-related genes in Drosophila, FlyGlycoDB provides spe ...

Axt Alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent ...

>>> !!! the repository is offline !!! The current successor is https://www.lovd.nl/USH1C. <<< The database contains all the variants published as pathogenic mutations in the international literature up to November 2007. In addition, unpublished Ushe ...

Labome organizes reagent information from high quality suppliers. The reagents include antibodies, siRNA/shRNA, ELISA kits, cDNA clones, proteins/peptides, and biochemicals. To help solve the antibody quality problem, Labome manually curates antibody ...

The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in p ...

SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects ...

The need for a way to represent genes/gene products separately from annotations, as well as the need to use the evidence ontology has lead to the creation of the GPAD (Gene Product Annotation Data) and GPI (Gene Product Information) formats. Whilst G ...

XGMML (eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. XGMML uses tags to describe nodes and edges of a graph. The purpose of XGMML is to make possible the exchange of graphs betw ...

The need for a way to represent genes/gene products separately from annotations, as well as the need to use the evidence ontology has lead to the creation of the GPAD (Gene Product Annotation Data) and GPI (Gene Product Information) formats, defined ...

The BpForms Grammar extends the IUPAC/IUBMB notation commonly used to represent unmodified DNA, RNA, and proteins to describe non-canonical forms of DNA, RNA, and proteins. Features include the representation of a wider range of monomeric forms, incl ...

>>>!!!<<< SMD has been retired. After approximately fifteen years of microarray-centric research service, the Stanford Microarray Database has been retired. We apologize for any inconvenience; please read below for possible resolutions to your querie ...

>>>!!!<<< The repository is inactive, please use SciLifeLab Data Repository >>>!!!<<< This DOI repository provides permanent identifiers to data sets generated by Life Science researchers active in Sweden, and for which no other suitable public ...

The Nomenclature and Symbolism for Amino Acids and Peptides, created by the IUPAC-IUB Joint Commission on Biochemical Nomenclature, formalizes the naming scheme for amino acids, non-peptide derivatives of amino acids and peptides as well as peptide d ...