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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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The Protein Interfaceome Database Resource Report Resource Website |
The Protein Interfaceome Database (RRID:SCR_002126) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2022. InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods. InterPare introduces a large-scale protein domain interaction interface database called InterPare. InterPare uses three methods: 1) the Euclidean distance method for checking the distance among subunits in multidomain proteins, 2) Accessible Surface Area (ASA) for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, 3) the Voronoi diagram, a computational geometry method, that uses a mathematical definition of interface regions. InterPare includes tools with different display modes for viewing protein interior, surface, and interaction interfaces. | protein interaction, structure | PMID:16122378 | Free, Freely Available | nif-0000-20921 | http://interpare.kobic.re.kr/index.html | SCR_002126 | InterPare | 2026-08-29 11:29:15 | 0 | |||||||
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NeuronBank Resource Report Resource Website |
NeuronBank (RRID:SCR_002004) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. Platform for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding. | encyclopedia, neuron, synapse, synaptic connection | has parent organization: Georgia State University; Georgia; USA | PMID:20428500 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00238, nif-0000-10901, SCR_005058 | SCR_002004 | NeuronBank wiki | 2026-08-29 11:29:11 | 0 | |||||||
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LSPD Resource Report Resource Website 1+ mentions |
LSPD (RRID:SCR_002125) | LSPD | data or information resource, database | LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus. | liver gene, promoter region, regulatory region, sequence, transcription | Free, Freely Available | nif-0000-20920 | SCR_002125 | The Liver Specific Gene Promoter Database | 2026-08-29 11:29:13 | 6 | ||||||||
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Target Protein Database Resource Report Resource Website |
Target Protein Database (RRID:SCR_002124) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. This database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents. At present all entries pertain to well-identified proteins that become adducted following defined exposures to known chemical agents in vivo or in cell culture experiments. Results from studies using enzymatic or chemical model systems have not been included but may be in the future. The search functions are relatively simple and intuitive, so most users can go straight to the Search page and begin searching. Additional explanations, examples and information about possible future expansions may be found. | chemically reactive metabolites, mammalian protein, xenobiotic agent | PMID:17367530 PMID:18823962 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20918 | SCR_002124 | TPDB | 2026-08-29 11:29:21 | 0 | ||||||||
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Subtilis Protein interaction Database Resource Report Resource Website |
Subtilis Protein interaction Database (RRID:SCR_002123) | SPiD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An online database of two-hybrid protein interactions in B. Subtilis. Interactions stored in SPID are either characterized by experimental evidence or by bibliographic references. A graphical user interface is provided to explore interaction networks as well as to view the details of each piece of evidence. The database contains 112 interactions between 79 proteins. | b. subtilis, protein, protein interaction | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20916 | SCR_002123 | Subtilis Protein interaction Database | 2026-08-29 11:29:21 | 0 | ||||||||
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PubGene Resource Report Resource Website 10+ mentions |
PubGene (RRID:SCR_002119) | data or information resource, database | It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. | gene, information, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is parent organization of: Coremine Medical |
Free, Freely Available | biotools:pubgene, nif-0000-20908 | https://bio.tools/pubgene | SCR_002119 | PubGene | 2026-08-29 11:29:21 | 39 | |||||||
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Aptamer Database - The Ellington Lab Resource Report Resource Website 1+ mentions |
Aptamer Database - The Ellington Lab (RRID:SCR_001781) | data or information resource, database | The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms. | aptamer, dna molecule, in vitro selection, ribozyme, rna molecule | has parent organization: University of Texas at Austin; Texas; USA | MURI DAAD19-99-1-0207; NIGMS 1R01 GM61789-01 |
PMID:14681367 | Free, Freely available | nif-0000-02558 | http://aptamer.icmb.utexas.edu | SCR_001781 | Aptamer Database, Ellington Lab Aptamer Database | 2026-08-29 11:29:11 | 3 | |||||
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Conserved Domain Database Resource Report Resource Website 100+ mentions |
Conserved Domain Database (RRID:SCR_002077) | CDD | data or information resource, database | Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments. | protein, amino acid sequence, nucleic acid, 3d structure, annotation, function, sequence, structure, amino acid, gold standard |
is used by: Mutation Annotation and Genomic Interpretation is listed by: re3data.org is related to: Pfam is related to: SMART is related to: COG is related to: NCBI Structure has parent organization: NCBI works with: Conserved Domains Search |
PMID:25414356 PMID:18984618 |
nif-0000-02647, r3d100010653 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd | SCR_002077 | Conserved Domains Database, Conserved Domains | 2026-08-29 11:29:14 | 358 | ||||||
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Spatially Constrained Parcellation Resource Report Resource Website 1+ mentions |
Spatially Constrained Parcellation (RRID:SCR_002198) | Spatially Constrained Parcellation | atlas, data or information resource, software resource | A set of tools for deriving region of interest (ROI) atlases by whole brain clustering of task or resting state data. This resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al., A whole brain fMRI atlas generated via spatially constrained spectral clustering, which is currently in revision in Human Brain Mapping. The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python, numpy and scipy to run. Source code and parcellations now available! Go to http://ccraddock.github.io/cluster_roi/ for more information. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155533 | SCR_002198 | 2026-08-29 11:29:14 | 4 | ||||||||
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Protein families database of alignments and HMMs Resource Report Resource Website 100+ mentions |
Protein families database of alignments and HMMs (RRID:SCR_002115) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that interaction are determined. The goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date. | bond, pfam, physical interaction, protein | PMID:9223186 PMID:18819075 |
Free, Freely available | nif-0000-20898 | http://ipfam.sanger.ac.uk/ | SCR_002115 | iPfam | 2026-08-29 11:29:21 | 307 | |||||||
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Protein-Small Molecule Database Resource Report Resource Website |
Protein-Small Molecule Database (RRID:SCR_002112) | PSMDB | data or information resource, database | Database of non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research. PSMB supports: * Support frequent updates - The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates. * Consider both protein and ligand structural redundancy - In the database, two complexes are considered redundant if they share a similar protein and ligand (the protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB. * Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database. * Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame). | drug, interaction, ligand, protein, small molecule, structure, protein-ligand binding | has parent organization: University of Toronto; Ontario; Canada | PMID:19153135 | Free, Available for download, Freely available | nif-0000-20897 | SCR_002112 | Protein - Small-Molecule DataBase | 2026-08-29 11:29:21 | 0 | ||||||
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Cell Signaling Pathways Resource Report Resource Website 1+ mentions |
Cell Signaling Pathways (RRID:SCR_002070) | data or information resource, database | Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research. | enzyme, gene, antibody, cell signaling, molecule, pathway, qpcr, research, sirna | PMID:17854489 | Free, Freely available | nif-0000-20825 | http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/PathFinder.html | SCR_002070 | PathFinder | 2026-08-29 11:29:12 | 6 | |||||||
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DBASS Resource Report Resource Website 1+ mentions |
DBASS (RRID:SCR_002107) | DBASS | data or information resource, database | A database of new exon boundaries induced by pathogenic mutations in human disease genes. | pathogen, mutation, disease gene, database, splice, mutation pattern, nucleotide structure, exon boundary, aberrant 3' splice site, aberrant 5' splice site |
is listed by: OMICtools has parent organization: University of Southampton; Southampton; United Kingdom |
PMID:20929868 PMID:16963498 PMID:16141195 PMID:17576681 |
Free, Freely available | OMICS_01883 | http://www.dbass.org.uk/ | SCR_002107 | 2026-08-29 11:29:12 | 2 | ||||||
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NIH Rat Genomics and Genetics Resource Report Resource Website |
NIH Rat Genomics and Genetics (RRID:SCR_002267) | data or information resource, database | The Rat Genome Program was launched after the National Institutes of Health (NIH) realized the potential of rat models in understanding basic biology and human health and disease. The purpose of this NIH Rat Genomics and Genetics web site is to serve as a central point for information on NIH sponsored and related rat genetic and genomic activities and resources. It will provide information on: the follow up to recommendations made to the NIH; funding opportunities for rat genomic and genetic tools and resources; major rat genomic resources available and/or produced in response to the NIH Rat Program; courses and meetings related to rat genomics and genetics; and selected reports and publications. These programs have produced a wide variety of resources and a way to link and capitalize upon the data and resources of other model organisms and the human. In conjunction with and in addition to these programs, the NIH, through the RGWG, has convened advisory groups and workshops to discuss the opportunities that rat models offer and provide recommendations on the investments that are needed to capitalize on these opportunities. | biology, disease, genome, human health, model, rat | nif-0000-20991 | SCR_002267 | RGS | 2026-08-29 11:29:16 | 0 | ||||||||||
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CPDB - the Circular Permutation Database Resource Report Resource Website |
CPDB - the Circular Permutation Database (RRID:SCR_002261) | CPDB | data or information resource, database |
A database of circular permutation (CP) in proteins that provides resources for studying circular permutation (CP) and circular permutation relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments. |
circular permutation, circular permutation site prediction, cp cluster, cp site prediction, permutant, protein structure | has parent organization: National Tsing Hua University; Hsinchu; Taiwan | National Science Council Taiwan 96-3112-B-007-006; National Science Council Taiwan 97-2752-B-007-003-PAE |
PMID:18842637 | nif-0000-02693 | SCR_002261 | Circular Permutation Database | 2026-08-29 11:29:14 | 0 | ||||||
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COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic, https://bio.tools/cosmic | SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-08-29 11:29:16 | 4809 | |||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
ARUK ; British Heart Foundation ; EMBL ; NCI ; NCRR P20 RR016472; NEI ; NHGRI P41 HG02273; NHGRI U24 HG007722; NHGRI U41 HG006104; NHLBI ; NIAID ; NIA ; NIDDK ; NIGMS 5R01GM080646; NIGMS R01 GM080646; NIMH ; NLM G08 LM010720; NSF DBI-0850319; PDUK |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-08-29 11:29:17 | 19823 | |||||
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Neocortical Microcircuit Database Resource Report Resource Website |
Neocortical Microcircuit Database (RRID:SCR_002415) | NMDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic connections are characterized in terms of their physiological and anatomical profiles. Neuron morphology profiles are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles) and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of stimulation protocols applied to the presynaptic neuron (se-Profile). | electrophysiologythis site will provide a major resource for those interested in cortical microcircuitry once it is complete. it currently has almost 300 neuronal reconstructions and 176 connections mapped., gene expression, 3d reconstruction, analysis tools, connectivity, cortical neuron, intracellular injection, intracellular recording, microcircuit, microcircuitry, microscopy, neurolucida, neuron morphology, rat, synaptic connectivity | has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland | PMID:15923726 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00124 | SCR_002415 | 2026-08-29 11:29:23 | 0 | |||||||
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Scholarly Open Access Resource Report Resource Website 10+ mentions |
Scholarly Open Access (RRID:SCR_002650) | Scholarly OA | blog, data or information resource, narrative resource | Blog featuring critical analysis of scholarly open-access journals by Jeffrey Beale. Good tool to consult if you have suspicions that a journal is less than legit. Jeffrey Beall works as a librarian at Auraria Library, University of Colorado Denver, in Denver, Colorado. | open access | is listed by: FORCE11 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156078 | SCR_002650 | 2026-08-29 11:29:18 | 12 | ||||||||
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Human Proteomics Initiative Resource Report Resource Website |
Human Proteomics Initiative (RRID:SCR_002373) | HPI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals. | function, gene, alignment, biologist, clustering, coding, development, genome, human, location, mammalian, modification, ortholog, population, post-translational, protein, proteome, proteomic, proteomics, sequence, splice, structure, subcellular, variant, variation, gold standard |
is related to: UniProt Chordata protein annotation program has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:11301130 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21199 | SCR_002373 | Human Proteome Initiative, UniProtKB/Swiss-Prot Human Proteome Initiative | 2026-08-29 11:29:23 | 0 |
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