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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NINDS ; NIDDK ; European Molecular Biology Laboratory ; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; NBDC - National Bioscience Database Center ; Japan Science and Technology Agency |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-07-28 09:41:37 | 1215 | ||||
|
Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | data set, data or information resource, organization portal, consortium, portal | Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present. | genome, sequencing, protein, rna, dna, consortium |
is related to: modENCODE is related to: ENCODE is related to: 3D Genome has parent organization: Stanford University; Stanford; California has parent organization: University of California at Santa Cruz; California; USA |
NHGRI HG006992 | PMID:15499007 | Free, Freely available | SCR_015482 | ENCODE Project | 2026-07-28 09:43:51 | 1244 | |||||||
|
RNAcompete Resource Report Resource Website 1+ mentions |
RNAcompete (RRID:SCR_015900) | software application, software resource, data analysis software, data processing software | Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rna, protein, interaction, binding, preference, rna-seq, recognition, rbp, k-mer, structured rna, unstructured rna, matlab |
uses: MATLAB has parent organization: University of Toronto; Ontario; Canada |
CIHR MOP-49451; CIHR MOP-14609; CIHR MOP-93671; Natural Sciences and Engineering Research Council ; Canadian Foundation of Innovation ; Ontario Genomics Institute ; Ontario Research Fund ; National Science and Engineering Research Council of Canada (NSERC) |
PMID:19561594 PMID:27956239 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_18668 | SCR_015900 | RNAcompete Tool | 2026-07-28 09:44:10 | 1 | ||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | software application, data analysis software, software resource, data processing software, data visualization software | Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments. | cytoscape, cluepedia, search tool, marker, pathway, experimental data, in silico data, linear dependence, gene, protein, miRNA | is a plug in for: Cytoscape | INCa ; Canceropole Ile de France ; INSERM ; MedImmune ; Qatar National Research Fund NPRP09-1174-3-291; European Commission 7FP Geninca 202230); LabEx Immuno-Oncology |
PMID:23325622 | Free for non-profits, Free for academic use, Available for download, Commercially available, Available for purchase | SCR_015784 | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-07-28 09:44:01 | 192 | |||||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | software application, standalone software, web application, software resource | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02; Desarrollo e Innovación Tecnológica |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | 2026-07-28 09:44:04 | 2020 | ||||||||
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BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | service resource, data or information resource, data repository, database, storage service resource | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U41HG006673; NIDDK K01 DK098285; Canadian Institutes for Health Research |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-07-28 09:44:14 | 1355 | ||||||
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mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | software application, web application, data analysis software, data or information resource, database, software resource, data processing software | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha, https://doi.org/10.17616/R3SP8V | SCR_016148 | 2026-07-28 09:44:06 | 149 | ||||||||
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Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | software application, data analysis software, sequence analysis software, software resource, data processing software, data visualization software | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | 2026-07-28 09:44:05 | 37 | ||||||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | software application, data analysis software, sequence analysis software, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-07-28 09:44:13 | 66 | ||||
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DOMALIGN Resource Report Resource Website |
DOMALIGN (RRID:SCR_016085) | software application, software resource, data processing software, alignment software, image analysis software | Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. | protein, domain, alignment, embassy, dhf, daf, fragment, redundancy, psi-blast | is listed by: Debian | Free, Available for download | https://sources.debian.org/src/embassy-domalign/ | SCR_016085 | Embassy-domalign | 2026-07-28 09:44:04 | 0 | ||||||||
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Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | cassiopee-c | 2026-07-28 09:44:12 | 0 | |||||||
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ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | software application, data analysis software, software resource, data processing software, standalone software, software toolkit | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-07-28 09:44:11 | 10 | ||||||||||
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REmAb Resource Report Resource Website |
REmAb (RRID:SCR_016239) | service resource, biomaterial analysis service, production service resource, material analysis service, analysis service resource | Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line. | mass, spectrometry, monoclonal, anitbody, protein, sequencing, cell, line | Commercially available, Free consultation | SCR_016239 | Antibody Sequencing Service | 2026-07-28 09:44:09 | 0 | ||||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, service resource, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-07-28 09:44:07 | 35 | |||||||||
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ARNIE Resource Report Resource Website |
ARNIE (RRID:SCR_000514) | ARNIE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. | network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
MRC ; Wellcome Trust |
PMID:20802085 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01529 | SCR_000514 | AVEXIS Receptor Network with Integrated Expression | 2026-07-28 09:40:00 | 0 | |||||
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Windber Tissue Bank Resource Report Resource Website |
Windber Tissue Bank (RRID:SCR_000509) | WRI Tissue Bank | tissue bank, biomaterial supply resource, material resource | Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmicro system, which permits the pathologist to remotely view, navigate and share images at sub-micron resolution over standard internet connections in real-time. | specimen, clinical data, family history, demographic data, tissue, plasma, serum, dna, rna, protein, optimum cutting temperature, formalin fixed paraffin embedded, frozen, normal, disease |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Windber Research Institute |
Normal, Disease | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_29009 | SCR_000509 | Windber Research Institute Tissue Bank, Windber Research Institute Tissue Banking, Windber Tissue Banking, WRI Tissue Banking | 2026-07-28 09:40:00 | 0 | ||||||
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Protein-Protein Interactions Table for Human herpesvirus 1 Resource Report Resource Website |
Protein-Protein Interactions Table for Human herpesvirus 1 (RRID:SCR_000397) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The scope of the project includes molecular information pertaining to oral pathogens, bacterial and viral. The website contains a table of protein-protein interactions for human herpesvirus 1. It is operated for the U.S. Department of Energy's National Nuclear Security Administration. | bacterial, herpesvirus 1, pathogen, protein, viral | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20905 | http://semiglobe.lanl.gov/microbe.php?class=virus | SCR_000397 | HSV1 PPI | 2026-07-28 09:39:59 | 0 | ||||||||
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eSLDB - eukaryotic Subcellular Localization database Resource Report Resource Website 1+ mentions |
eSLDB - eukaryotic Subcellular Localization database (RRID:SCR_000052) | eSLDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions. | proteome, protein, homology | has parent organization: University of Bologna; Bologna; Italy | European Union VI Framework Programme | PMID:17108361 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02815 | SCR_000052 | eukaryotic Subcellular Localization database | 2026-07-28 09:39:55 | 1 | |||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-07-28 09:40:04 | 2 | |||||||
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Collecting Duct Database Resource Report Resource Website |
Collecting Duct Database (RRID:SCR_000759) | CDDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct. | expressed sequence tag, expression, family, functional, gene, aquaporin, array, cdna, classification, collecting duct, homologous, human, kidney, literature, mammal, mammalian, microarray, mouse, protein, protein localization and targeting databases, rat, receptor, regulatory, relationship, scan, serial analysis, specie, target, tissue, transporter, vasopressin, water channel protein | has parent organization: National Institutes of Health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21078 | SCR_000759 | Collecting Duct Database | 2026-07-28 09:40:04 | 0 |
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