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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Parasite Databases of Clustered ESTs Resource Report Resource Website 1+ mentions |
Parasite Databases of Clustered ESTs (RRID:SCR_002262) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. These databases were constructed by extracting the organism specific ESTs from dbEST, removing polyA sequences from the ends and trimming 5' and 3' regions with greater than 25% N's in a 20 base pair window. These quality sequences were then aligned using the cap2 program and the consensus sequences thus generated put into a database that is available on the web. A number of parasitic organisms were chosen that have between 3000 and 15000 ESTs. The attempt here is to provide useful information and analyses to the scientific community without curating the results in any way. A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets. | est, expression, fungus, gene, animal, apicomplexa, biological, organism, parasitic, phylum, plants, polya, protein, sequence, therapeutic | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20980 | SCR_002262 | PDCEST | 2026-07-28 09:40:35 | 2 | |||||||||
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Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-07-28 09:40:25 | 1 | |||||
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CORUM Resource Report Resource Website 100+ mentions |
CORUM (RRID:SCR_002254) | CORUM | data or information resource, database |
Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded. The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
mammalian protein, protein, protein complex, protein function, FASEB list |
is listed by: OMICtools is related to: Interaction Reference Index is related to: ConsensusPathDB has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
BMBF 031U212C | PMID:19884131 PMID:17965090 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02688, OMICS_01904, r3d100011272 | http://mips.gsf.de/genre/proj/corum | SCR_002254 | CORUM the Comprehensive Resource of Mammalian protein complexes, CORUM - the Comprehensive Resource of Mammalian protein complexes | 2026-07-28 09:40:35 | 163 | ||||
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Knowledgebase for Addiction Related Genes Resource Report Resource Website 1+ mentions |
Knowledgebase for Addiction Related Genes (RRID:SCR_002687) | KARG | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download. | molecular neuroanatomy resource, gwas, meta-analysis, genetic susceptibility, gene, protein, chromosome, pathway, drug of abuse, blast, addiction, substance abuse, drug abuse, microarray, proteomics, qtl, population association, genetic linkage |
uses: PubMed has parent organization: Peking University; Beijing; China |
PMID:18179280 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00411 | SCR_002687 | KARG: Knowledgebase for Addiction-Related Gene, Knowledgebase for Addiction-Related Gene, KARG: Knowledgebase for Addiction Related Genes | 2026-07-28 09:40:39 | 8 | ||||||
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WD repeat Family of Proteins Resource Report Resource Website |
WD repeat Family of Proteins (RRID:SCR_002160) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. This website contains a library of WD-repeat containing proteins in which the repeats appear as multi-aligned sets. WD-repeat-containing proteins are those that contain 4 or more copies of the WD-repeat (tryptophan-aspartate repeat), a sequence motif approximately 31 amino acids long, that encodes a structural repeat. This repeat is described by the following profile, where x is ANY amino acid. By clicking on each high-lighted character you will obtain the distribution of amino acids found at that position of the repeat among an aligned set of WD-repeat containing proteins. The tertiary structure of only one member of this family has been determined, that of the G protein beta subunit, which contains 7 WD-repeats. Each of the 7 repeats folds into a small antiparallel beta-sheet. The over-lines above indicate the position of these strands, with a being the strand closest to the central pore and d at the external surface of the folded protein. These sheets are arranged around a central pseudosymmetry axis into a beta propeller. The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases. | eukaryotic, function, genetic, align, amino acid, ancient, antiparallel, aspartate, beta, cell, disease, domain, g protein, multi-aligned, organelle, origin, pathway, propeller, protein, proto, pseudosymmetry, sheet, structural, tertiary, tryptophan, wd-repeat | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20949 | SCR_002160 | WD repeat Family of Proteins | 2026-07-28 09:40:21 | 0 | |||||||||
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EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | EcoGene Database of Escherichia coli Sequence and Function | 2026-07-28 09:40:25 | 56 | |||
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object-oriented Transcription Factors Database Resource Report Resource Website 1+ mentions |
object-oriented Transcription Factors Database (RRID:SCR_002435) | data or information resource, database | ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers. | eukaryotic, expression, factor, gene, basal, binding site, biochemical, biology, cellular, complex, genome, genomic, information, interaction, molecule, monomer, multisubunit, nucleotide sequences, transcriptional regulator sites, transcription factors, object, polypeptide, process, prokaryotic, property, protein, protein-protein interaction, regulatory, sequence, transcription | has parent organization: IFTI-Mirage | PMID:10592257 PMID:9847215 PMID:9399874 |
Free, Freely available | nif-0000-21303 | SCR_002435 | ooTFD | 2026-07-28 09:40:26 | 2 | |||||||
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TcoF Resource Report Resource Website 10+ mentions |
TcoF (RRID:SCR_002158) | TcoF | data or information resource, database | Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). | protein, regulation, transcription, transcription factor, transcription co-factor, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:20965969 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tcof-db, OMICS_01865 | https://bio.tools/tcof-db | SCR_002158 | Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins, TcoF-DB, TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins | 2026-07-28 09:40:21 | 10 | |||||
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EyeSite Resource Report Resource Website 1+ mentions |
EyeSite (RRID:SCR_002669) | EyeSite | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An information and modeling database for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity. A principal feature of the site is structural annotations, which range from experimentally solved structures to close structural neighbors to distant structure predictions. Many pre-generated homology models are provided. Other features include domain architecture analysis and pre-generated sequence alignments, and the site is extensively linked to other bioinformatic resources on the web. | eye, protein, homology, ciliary body, cornea, fovea, iris, lens, optic nerve, retina, rpe choroid, trabecular meshwork | has parent organization: Birkbeck University of London; London; United Kingdom | MRC | PMID:14681381 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-02830 | SCR_002669 | EyeSite Database | 2026-07-28 09:40:29 | 1 | |||||
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Allopathfinder Resource Report Resource Website |
Allopathfinder (RRID:SCR_002702) | AlloPathFinder | software application, source code, software resource | Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure. | allosteric communication, allostery, allosteric, pathway, protein, residue, prediction, myosin, computational model, protein model, structure-based protein classification, protein classification, myosin allosteric communication |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; Jane Coffin Childs Memorial Fund ; NIGMS U54 GM072970; NIGMS GM33289 |
PMID:17900617 | Free, Available for download, Freely available | nif-0000-23327 | SCR_002702 | Predicting allosteric communication in myosin via a conserved residue pathway | 2026-07-28 09:40:30 | 0 | |||||
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DrugBank Resource Report Resource Website 5000+ mentions |
DrugBank (RRID:SCR_002700) | DrugBank | data or information resource, database | Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. | drug, target, pathway, structure, pharmacology, drug class, chemical, pharmaceutical, drug target, sequence, reaction, interaction, protein, proteome, blast, data analysis service, small molecule-protein, small molecule, clinical medicine, pharmacy, medicine, pharmaceutical biotechnology, cheminformatics, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is used by: In vivo - In silico Metabolite Database is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is related to: ConsensusPathDB is related to: PharmGKB Ontology is related to: Allen Institute Neurowiki is related to: Coremine Medical is related to: MalaCards is related to: PSICQUIC Registry is related to: DrugPort is related to: Integrated Manually Extracted Annotation has parent organization: University of Alberta; Alberta; Canada |
Genome Alberta ; Genome Canada ; GenomeQuest Inc. ; Canadian Institutes of Health Research |
PMID:16381955 PMID:21059682 PMID:18048412 |
Free, Freely available | nif-0000-00417, OMICS_01580, r3d100010544 | https://doi.org/10.17616/R3V60M | SCR_002700 | 2026-07-28 09:40:39 | 5122 | |||||
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Evolutionary Lineage Inferred from Structural Analysis Resource Report Resource Website 1+ mentions |
Evolutionary Lineage Inferred from Structural Analysis (RRID:SCR_002343) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind. | evolutionary, function, functional, analysis, annotation, atomic unit, calculation, comparative, domain, genomic, homology, modeling, place, probabilistic, protein, protein domain and protein classification databases, proteome, proteomic, sequence, structural, structure, template | has parent organization: Boston University; Massachusetts; USA | PMID:12952559 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21141 | SCR_002343 | ELISA | 2026-07-28 09:40:24 | 1 | |||||||
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Entrez Gene Resource Report Resource Website 1000+ mentions |
Entrez Gene (RRID:SCR_002473) | NCBI_Gene, NCBI Genen NCBI Entrez | data or information resource, database | Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available. | gene, gene expression, gene location, gene map, gene prediction, genome, genome sequence analysis, phenotype, nomenclature, gene mapping, protein, genetic code, function, annotation, gold standard, bio.tools |
is used by: Animal QTLdb is used by: NIF Data Federation is used by: LIPID MAPS Proteome Database is used by: DisGeNET is used by: Nowomics is used by: Cytokine Registry is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Vesiclepedia is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: Gene Reference into Function is related to: Integrated Molecular Interaction Database is related to: Biomine is related to: SEGS is related to: STOP is related to: Coremine Medical is related to: Consensus CDS is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: Array Information Library Universal Navigator is related to: biomaRt has parent organization: NCBI works with: Open Regulatory Annotation Database |
PMID:17148475 PMID:21115458 |
Free, Freely available | nif-0000-02801, biotools:entrez_gene, OMICS_01651, r3d100010650 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene, https://bio.tools/entrez_gene, https://doi.org/10.17616/R3603S | SCR_002473 | NCBI Gene, Gene - Gene mapped phenotypes, Gene - Gene and mapped phenotypes, Gene Database, GeneID | 2026-07-28 09:40:37 | 2830 | |||||
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RESID Resource Report Resource Website 10+ mentions |
RESID (RRID:SCR_003505) | RESID | data or information resource, database | A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. | protein cross-link, protein modification, protein structure, protein, structure, annotation, amino-terminal, carboxyl-terminal, peptide chain cross-link, post-translational modification, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:15174122 PMID:12520062 |
nif-0000-03400, r3d100000023, biotools:resid | https://bio.tools/resid, https://doi.org/10.17616/R3Z59M | http://www.ebi.ac.uk/RESID/ | SCR_003505 | RESID Database at the EBI, RESID Database at PIR, RESID Database of Protein Modifications, RESID Database | 2026-07-28 09:40:43 | 10 | |||||
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PINdb Resource Report Resource Website 1+ mentions |
PINdb (RRID:SCR_003348) | PINdb, PIN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Relational database containing the compositions of multi-protein complexes in the nucleus of budding yeast and human cells. Its content is limited to information curated from the proteomics literature and primarily comprises of components of the general transcription and DNA repair machinery. In addition to database browsing and searching capabilities, the PINdb web portal also includes user-friendly interactive tools for comparative analysis of the composition of multiple protein complexes and for clustering and visualizing network of protein complexes. Currently, PINdb contains mostly protein complexes that may be involved in gene transcription. To facilitate comparative analyses and identification of protein complexes, the compositional information is integrated with standardized gene nomenclature, annotation and protein sequences from public databases. The PINdb web interface provides a number of tools for (1) comparison of protein complexes, (2) search for a protein complex by its published name or by a partial list of its components and (3) browsing specific subsets or a functional classification of the complexes. | nuclear protein complex, protein interaction, targeted proteomics, network visualization, protein, nucleus, proteomics, protein complex, gene transcription | is related to: ConsensusPathDB | PMID:15087322 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03290 | SCR_003348 | Proteins Interacting in the Nucleus Database | 2026-07-28 09:40:42 | 4 | ||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, service resource, database | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-07-28 09:40:45 | 0 | ||||||
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HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-07-28 09:40:41 | 2 | |||||
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SynSysNet Resource Report Resource Website 1+ mentions |
SynSysNet (RRID:SCR_003180) | SynSysNet | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication. | gene, synapse, protein, interaction, compound, disease, structure, model, compound, protein-drug interaction, protein-protein interaction, pathway, drug-target, small molecule, interaction network, homology, drug, drug-target interaction, compound-protein interaction, visualization, proteomics, network |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
Huntington's disease, Chorea Huntington, Epilepsy, Multiple Sclerosis, Parkinson's disease, Schizophrenia, Neurological disease | European Union Seventh FPSYNSYS 242167; DFG GRK1772; DFG GRK1360 |
PMID:23143269 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156893, OMICS_01914 | SCR_003180 | SynSysNet - Synaptic Proteins Database | 2026-07-28 09:40:38 | 3 | ||||
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LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | data or information resource, database | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-07-28 09:40:35 | 3 | ||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, service resource, database | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-07-28 09:40:42 | 437 |
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