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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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STRING Resource Report Resource Website 10000+ mentions |
STRING (RRID:SCR_005223) | STRING | data or information resource, database | Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013) | protein association, protein functional association, protein interaction, protein-protein interaction, protein, sequence, protein sequence, interaction, gene, FASEB list |
is used by: MobiDB is used by: PAXdb is listed by: Nuclear Receptor Signaling Atlas is listed by: NIDDK Information Network (dkNET) is related to: Biomine is related to: PSICQUIC Registry is related to: ShinyGO has parent organization: European Molecular Biology Laboratory has plug in: Cytoscape StringApp |
BMBF ; European Union FP6 ; EMBO ; ProBioC ; Swiss Institute of Bioinformatics |
PMID:23203871 PMID:21045058 PMID:18940858 PMID:17098935 PMID:15608232 PMID:12519996 |
nif-0000-03503, r3d100010604 | https://doi.org/10.17616/R3VS40 | SCR_005223 | Search Tool for the Retrieval of Interacting Genes/Proteins, STRING - Known and Predicted Protein-Protein Interactions | 2026-07-28 09:41:18 | 29246 | |||||
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YMDB - Yeast Metabolome Database Resource Report Resource Website 10+ mentions |
YMDB - Yeast Metabolome Database (RRID:SCR_005890) | YMDB | data or information resource, database | 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 textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2027 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein. Users may search through the YMDB using a variety of database-specific tools. The simple text query supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the search for field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button generates a tabular synopsis of YMDB's content. This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the YMDB fields and sources is available. Under the Search link users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the YMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of YMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in YMDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. YMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of YMDB's reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS and NMR Spectra Search links. Users may download YMDB's complete textual data, chemical structures and sequence data by clicking on the Download button. | small molecule, metabolite, enzyme, transporter, gene, protein, chemical property, reaction, pathway, class, protein, proteome, blastp, nmr, ms spectra, chemical structure | has parent organization: University of Alberta; Alberta; Canada | Canadian Institutes of Health Research | PMID:22064855 | Freely available - Explicit permission / acknowledgment of the source material and original publication is required for commercial purposes. We ask users who download significant portions of the database cite the YMDB paper in any resulting publications. | nlx_151612, r3d100012733 | https://doi.org/10.17616/R3Z51K | SCR_005890 | Yeast Metabolome Database (YMDB), Yeast Metabolome Database | 2026-07-28 09:41:31 | 14 | ||||
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Unified Human Interactome Resource Report Resource Website 10+ mentions |
Unified Human Interactome (RRID:SCR_005805) | UniHI | data or information resource, database | A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks. | molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, network |
is listed by: OMICtools has parent organization: University of Algarve; Faro; Portugal |
PMID:24214987 PMID:22218860 PMID:18984619 PMID:17158159 |
Public, Non-commercial | OMICS_01911, nif-0000-03609 | http://www.mdc-berlin.de/unihi | SCR_005805 | 2026-07-28 09:41:21 | 19 | ||||||
|
ChIPBase Resource Report Resource Website 100+ mentions |
ChIPBase (RRID:SCR_005404) | ChIPBase | data or information resource, database | A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chip-seq, gene, rna, microrna, long non-coding rna, non-coding, transcription factor binding site, protein, transcriptional regulation, annotation, regulatory element, transcription factor, genome, network, FASEB list |
is listed by: OMICtools has parent organization: Sun Yat-sen University; Guangdong; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00527 | SCR_005404 | 2026-07-28 09:41:19 | 145 | ||||||||
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TopoSNP Resource Report Resource Website 1+ mentions |
TopoSNP (RRID:SCR_005572) | TopoSNP | data or information resource, database | A topographic database for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. It also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. | visualization, disease, non-disease, non-synonymous single nucleotide polymorphism, topographic mapping, single nucleotide polymorphism, 3d structure, protein, protein structure, coding region, entropy |
is listed by: OMICtools is related to: OMIM is related to: dbSNP is related to: Pfam is related to: Clustal W2 has parent organization: University of Illinois at Chicago; Illinois; USA |
NSF DBI0133856; NSF DBI0078270; NSF MCB998008; NIGMS GM68958 |
PMID:14681472 | nif-0000-03570, OMICS_00191 | SCR_005572 | topographic mapping of Single Nucleotide Polymorphism | 2026-07-28 09:41:17 | 4 | ||||||
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DOMMINO - Database Of MacroMolecular INteractiOns Resource Report Resource Website 1+ mentions |
DOMMINO - Database Of MacroMolecular INteractiOns (RRID:SCR_005958) | DOMMINO | data or information resource, database | DOMMINO is a comprehensive structural database on macromolecular interactions. As of June, 2011, it contains more than 407,000 binary interactions. The distinctive features of DOMMINO are: # Automated updates: DOMMINO is fully automated and is designed to update itself on a weekly basis, one day after a PDB weekly update. Thus, the community will be able to study macromolecular interactions almost immediately after they are released by PDB. # Coverage of non-domain mediated interactions: In addition to domain-domain and domain-peptide interactions the database characterizes the interaction between domains and unstructured protein regions that are not parts of a domain, such as inter-domain linkers and N- and C-termini. The interactions that involve the latter unstructured parts of proteins have been included to the database for the first time providing additional ~186,000 interactions (~45% of the total number of interactions, as of June, 2011). # Coverage of new structural domains: DOMMINO employs one of the most accurate structural classifications of proteins, SCOP. In addition to the existing SCOP-annotated domains, we employ a state-of-the-art machine learning approach to classify newer protein structures into existing SCOP families. With the progress of structural genomics, we do not expect a significant growth of the number of structurally novel folds or protein families and therefore our method allows covering almost all new protein structures. In total, using this predictive approach has allowed us to add more than 261,000 new interactions, almost twice as many as existing SCOP-annotated interactions. # The web-interface is designed to give the user a possibility of a flexible search as well as the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level. The web interface of the DOMMINO database includes a comprehensive list of help topics linked to the specific actions. In addition, we have designed a step-by-step tutorial that covers all aspects of working with the data from DOMMINO using the web interface. | macromolecular interaction, macromolecule, structural domain, non-domain mediated interaction, protein, domain, peptide, interaction, protein-protein interaction, protein-peptide interaction, protein-dna interactions, protein-rna interactions, rna-rna interactions, rna-dna interactions, interface structure, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: SCOP: Structural Classification of Proteins has parent organization: University of Missouri; Missouri; USA |
NSF DBI-0845196 | PMID:22135305 | biotools:dommino, nlx_151316 | http://orion.rnet.missouri.edu/~nz953/DOMMINO/, https://bio.tools/dommino | SCR_005958 | Database Of MacroMolecular INteractiOns | 2026-07-28 09:41:30 | 1 | |||||
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CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | data or information resource, database | The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. | protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute |
NHGRI R01 HG004881; NIAID contract HHSN266200100038C |
PMID:22140108 | biotools:charprotdb, nlx_149421 | https://bio.tools/charprotdb | SCR_005872 | Characterized Protein Database | 2026-07-28 09:41:22 | 0 | |||||
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VirHostNet: Virus-Host Network Resource Report Resource Website 1+ mentions |
VirHostNet: Virus-Host Network (RRID:SCR_005978) | VirHostNet | data or information resource, database | Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy. | interaction, protein, virus, protein-protein interaction, protein interaction, infectious disease, antiviral drug design, proteome, interactome, molecular function, cellular pathway, protein domain, virus-virus, virus-host, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: VirusMINT is related to: IntAct is related to: HIV-1 Human Protein Interaction Database is related to: PSICQUIC Registry has parent organization: Claude Bernard University Lyon 1; Lyon; France |
PMID:18984613 | Acknowledgement requested, Public | nif-0000-03634, OMICS_01910, biotools:virhostnet | https://bio.tools/virhostnet | SCR_005978 | Virus-Host Network | 2026-07-28 09:41:31 | 6 | |||||
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Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-07-28 09:41:38 | 64 | |||
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DroID - Drosophila Interactions Database Resource Report Resource Website 10+ mentions |
DroID - Drosophila Interactions Database (RRID:SCR_006634) | DroID | data or information resource, database | A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available. | interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, ortholog |
is listed by: OMICtools is related to: Cytoscape has parent organization: Wayne State University School of Medicine; Michigan; USA |
PMID:21036869 PMID:18840285 |
Free, Public, Acknowledgement requested | nif-0000-02767, OMICS_01908 | SCR_006634 | DroID - The Drosophila Interactions Database | 2026-07-28 09:41:36 | 35 | ||||||
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ProRepeat Resource Report Resource Website 1+ mentions |
ProRepeat (RRID:SCR_006113) | ProRepeat | data or information resource, database | ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons. | amino acid, tandem, repeat, protein, sequence, nucleotide sequence, repeat fragment, protein repeat, proteome, sequence length, gene, taxon, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB is related to: RefSeq has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
PMID:22102581 | nlx_151587, biotools:prorepeat | https://bio.tools/prorepeat | SCR_006113 | 2026-07-28 09:41:27 | 1 | |||||||
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ProtChemSI Resource Report Resource Website 1+ mentions |
ProtChemSI (RRID:SCR_006115) | ProtChemSI | data or information resource, database | The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly. | protein, chemical, 3d structure, biological network, interaction, ligand, prediction, fasta, fasta sequence, smiles string, complex, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:21573205 | Acknowledgement requested | nlx_151590, biotools:protchemsi | https://bio.tools/protchemsi | SCR_006115 | Protein-Chemical Structural Interactions, ProtChemSI: protein-chemical interaction database, ProtChemSI - the database of protein-chemical structural interactions | 2026-07-28 09:41:31 | 3 | |||||
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HotRegion - A Database of Cooperative Hotspots Resource Report Resource Website 1+ mentions |
HotRegion - A Database of Cooperative Hotspots (RRID:SCR_006022) | HotRegion | data or information resource, database | Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. HotRegion provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. The number of interfaces in the database is 147909 and still growing. | residue, chain, complex, monomer, pair potential, hotspot, hotregion, accessible surface area, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Koc University; Istanbul; Turkey |
Turkish Academy of Sciences ; TUBITAK 109T343; TUBITAK 109E207 |
PMID:22080558 | nlx_151420, biotools:hotregion | https://bio.tools/hotregion | SCR_006022 | HotRegion: a database of predicted hot spot clusters, HotRegion: A database of cooperative hot spots | 2026-07-28 09:41:25 | 5 | |||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 | SCR_006433 | 2026-07-28 09:41:34 | 725 | |||||
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Scansite Resource Report Resource Website 100+ mentions |
Scansite (RRID:SCR_007026) | data or information resource, database | Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. The Motifscanner program utilizes an entropy approach that assesses the probability of a site matching the motif using the selectivity values and sums the logs of the probability values for each amino acid in the candidate sequence. The program then indicates the percentile ranking of the candidate motif in respect to all potential motifs in proteins of a protein database. When available, percentile scores of some confirmed phosphorylation sites for the kinase of interests or confirmed binding sites of the domain of interest are provided for comparison with the scores of the candidate motifs. | binding, kinase, phosphorylate, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
biotools:scansite, nif-0000-20914 | https://bio.tools/scansite | SCR_007026 | Scansite | 2026-07-28 09:41:40 | 297 | ||||||||
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HIstome: The Histone Infobase Resource Report Resource Website 1+ mentions |
HIstome: The Histone Infobase (RRID:SCR_006972) | HIstome | data or information resource, database | Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune. | histone, protein, enzyme, modifying enzyme, post-translational modification, variant, promoter region, gene, epigenetic regulation, india, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: ACTREC - Advanced Centre for Treatment Research and Education in Cancer |
Cancer | ACTREuropean Union - Advanced Centre for Treatment Research and Education in Cancer ; Government of India |
PMID:22140112 | Free, Public, Acknowledgement requested | biotools:histome, r3d100010977, nlx_151419 | http://www.actrec.gov.in/histome/, https://bio.tools/histome, https://doi.org/10.17616/R3RD0R | http://www.histome.net/ | SCR_006972 | 2026-07-28 09:41:42 | 1 | |||
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HPRD - Human Protein Reference Database Resource Report Resource Website 1000+ mentions |
HPRD - Human Protein Reference Database (RRID:SCR_007027) | HPRD | data or information resource, database | Database that 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 human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. | protein, disease, network, post-translational, proteome, protein binding, protein s, protein c, pathway, protein-protein interaction, protein expression, subcellular localization, phosphorylation motif, signaling pathway, protein sequence, blast, molecule, domain, motif, post-translational modification, protein isoform, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEMINI is listed by: re3data.org is related to: Human Proteinpedia is related to: MatrixDB is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: Gene Ontology is related to: Agile Protein Interactomes DataServer has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18988627 PMID:16381900 PMID:14525934 |
Acknowledgement requested, Free, Non-commercial, Commercial requires license | nif-0000-00137, r3d100010978 | https://doi.org/10.17616/R3MK9N | SCR_007027 | Human Protein Reference Database | 2026-07-28 09:41:42 | 1266 | |||||
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Therapeutic Target Database Resource Report Resource Website 10+ mentions |
Therapeutic Target Database (RRID:SCR_006892) | TTD | data or information resource, database | A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets. Also included in this database are links to relevant databases that contain information about the function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and related literatures of each target.This database currently contains 1535 targets and 2107 drugs/ligands. Queries can be submitted by entering or selecting the required information in any one or combination of the five fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. | therapeutic, protein, nucleic acid, disease, pathway, drug, ligand, target, FASEB list |
is listed by: OMICtools is related to: ConsensusPathDB has parent organization: National University of Singapore; Singapore; Singapore |
nif-0000-03596, OMICS_01593 | http://bidd.nus.edu.sg/group/cjttd/ | SCR_006892 | 2026-07-28 09:41:38 | 44 | ||||||||
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MitoInteractome Resource Report Resource Website |
MitoInteractome (RRID:SCR_010225) | MitoInteractome | data or information resource, database | Database that gathers data on interactions in the mitochondrial proteome that has been used to construct a network for the aging process in humans and to identify interactions that influence this process, since mitochondria is a major source of cellular reactive oxygen species that accumulate during aging. It will: # aid in increasing our understanding of the molecular functions and interaction networks of mitochondrial proteins, # help in identifying new target proteins for experimental research using predicted protein-protein interaction information, and # help in identifying biomarkers for diagnosis and new molecular targets for drug development related to mitochondria. How is MitoInteractome different? * Provides protein-protein interaction information with graphical display. * Applies newly added new mitochondrial protein information by using BLAST incorporated in Mitointeractome * Shows correlation of mutation with their impact * Provides specific pathway information to aid study of their impact * Contains SNP Information | interaction, mitochondrial proteome, mitochondria, protein-protein interaction, physico-chemical property, polymorphism, protein sequence, protein, disease, snp, pathway | has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea | Aging | PMID:19958484 | nlx_156772 | SCR_010225 | MitoInteractome - Mitochondrial Protein Interactome Database | 2026-07-28 09:42:41 | 0 | ||||||
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UniPathway Resource Report Resource Website 10+ mentions |
UniPathway (RRID:SCR_010513) | UniPathway | data or information resource, database | A manually curated database of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. Users may do a quick search, browse pathway, browse compound, or browse organism. | metabolic pathway, pathway annotation, pathway, annotation, chemical reaction, protein, compound |
is related to: UniProtKB has parent organization: PrabiG has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal Government ; GIS-IBISA ; European Union SISYPHE ; European Union SLING 226073; European Union Microme 222886-2; French Government ANR MIRI BLAN08-1335497 |
PMID:22102589 | nlx_16723 | SCR_010513 | UniPathway: a metabolic door to UniProtKB/Swiss-Prot, UniPathway: a resource for the exploration of metabolic pathways | 2026-07-28 09:42:47 | 17 |
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