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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-09-12 12:57:52 | 779 | ||||
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Virus Pathogen Resource (ViPR) Resource Report Resource Website 100+ mentions |
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) | ViPR | data or information resource, data processing software, data repository, data visualization software, database, service resource, software application, software resource, storage service resource | Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. | flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list |
is recommended by: National Library of Medicine is listed by: Data and Computational Resources to Address COVID-19 is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
COVID-19 | NIAID | Restricted | nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 | http://www.viprbrc.org/, https://doi.org/10.17616/r30p93, https://doi.org/10.35083/, https://doi.org/10.35084/, https://dx.doi.org/10.35083/, https://dx.doi.org/10.35084/, https://fairsharing.org/10.25504/FAIRsharing.2qx8n8 | SCR_012983 | Virus Pathogen Resource, ViPR | 2026-09-12 12:57:56 | 173 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-09-12 12:58:02 | 1324 | ||||||
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BioIE: Extracting Informative Sentences From the Biomedical Literature Resource Report Resource Website 1+ mentions |
BioIE: Extracting Informative Sentences From the Biomedical Literature (RRID:SCR_013464) | data or information resource, database, software resource, software toolkit | BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases. | family, function, biomedical, context, disease, distribution, literature, medline interfaces, mesh-term, microarray, n-gram, protein, semantic, structure, syntactic | has parent organization: University of Manchester; Manchester; United Kingdom | nif-0000-21055 | SCR_013464 | BioIE | 2026-09-12 12:58:03 | 2 | |||||||||
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MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | data analysis software, data processing software, software application, software resource | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | MSStats | 2026-09-12 12:58:15 | 239 | ||||||
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-09-12 12:58:19 | 3874 | |||||
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Relibase Resource Report Resource Website 1+ mentions |
Relibase (RRID:SCR_014888) | data or information resource, database, software resource, web application | Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions. | structural biology, protein, ligand, protein data bank, pdb, visualization, analysis, molecular recognition | Available to the academic community | SCR_014888 | 2026-09-12 12:58:22 | 5 | |||||||||||
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Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure. | Protein structure prediction, protein, structure prediction, prediction service, automated prediction, analysis tools, genomic data, protein sequence, protein model, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:15215442 | Restricted | biotools:robetta | https://bio.tools/robetta | SCR_018805 | 2026-09-12 12:59:06 | 487 | |||||||
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FALCON Resource Report Resource Website 100+ mentions |
FALCON (RRID:SCR_018804) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction. | Protein structure, protein structure prediction, simulation, 3D structure, protein, high throughput protein, structure prediction | Restricted | SCR_018804 | FALCON@home | 2026-09-12 12:59:06 | 432 | ||||||||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626; NIGMS ; NIH Common Fund |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-09-12 12:59:08 | 7 | |||||||
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PROCHECK Resource Report Resource Website 100+ mentions |
PROCHECK (RRID:SCR_019043) | data analysis software, data processing software, software application, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-09-12 12:59:09 | 122 | |||||||||
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ConPlot Resource Report Resource Website 1+ mentions |
ConPlot (RRID:SCR_019216) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein. | Residue contact predictions, protein, secondary structure predictions, transmembrane helical topology, sequence conservation, protein bioinformatics, analysing data |
is related to: CCP4 has parent organization: University of Liverpool; Liverpool; United Kingdom |
Restricted | SCR_019216 | 2026-09-12 12:59:11 | 2 | ||||||||||
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PiMS Resource Report Resource Website 100+ mentions |
PiMS (RRID:SCR_011816) | PiMS | software resource | Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes. | protein | is listed by: OMICtools | BBSRC ; CCP4 ; Instruct |
PMID:21385349 | Free for academic use | OMICS_01010 | SCR_011816 | Protein Information Management System | 2026-09-12 12:57:40 | 190 | |||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | analysis service resource, data analysis service, production service resource, service resource, simulation software, software application, software resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-09-12 12:57:42 | 1 | ||||||
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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-09-12 12:57:44 | 0 | |||||||
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RNAcompete Resource Report Resource Website 1+ mentions |
RNAcompete (RRID:SCR_015900) | data analysis software, data processing software, software application, software resource | 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 |
Canadian Foundation of Innovation ; CIHR MOP-14609; CIHR MOP-49451; CIHR MOP-93671; National Science and Engineering Research Council of Canada (NSERC) ; Natural Sciences and Engineering Research Council ; Ontario Genomics Institute ; Ontario Research Fund |
PMID:19561594 PMID:27956239 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_18668 | SCR_015900 | RNAcompete Tool | 2026-09-12 12:58:32 | 1 | ||||||
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CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | data analysis software, data processing software, data visualization software, software application, software resource | 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 | 2026-09-12 12:58:30 | 193 | |||||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
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 | 2026-09-12 12:58:34 | 71 | ||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | software application, software resource, standalone software, web application | 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 | Desarrollo e Innovación Tecnológica ; Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02 |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | 2026-09-12 12:58:32 | 2043 | ||||||||
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DOMALIGN Resource Report Resource Website |
DOMALIGN (RRID:SCR_016085) | alignment software, data processing software, image analysis software, software application, software resource | 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 | 2026-09-12 12:58:35 | 0 |
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