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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ConPlot Resource Report Resource Website 1+ mentions |
ConPlot (RRID:SCR_019216) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | 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 | 2026-08-03 09:37:11 | 2 | ||||||||||
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CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. | transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools |
is listed by: Debian is listed by: bio.tools works with: PDBTM works with: Topology Data Bank of Transmembrane Proteins works with: TopDom |
Hungarian Scientific Research Fund | PMID:25943549 | Free, Freely available | biotools:cctop | https://bio.tools/cctop | SCR_016963 | CCTOP, Consensus Constrained TOPology | 2026-08-03 09:36:40 | 29 | ||||
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Illuminating the Druggable Genome Resource Report Resource Website 10+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | organization portal, data repository, portal, data or information resource, storage service resource, consortium, service resource | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-08-03 09:36:58 | 45 | |||||
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Collaborative Computing Project for NMR Resource Report Resource Website 10+ mentions |
Collaborative Computing Project for NMR (RRID:SCR_016983) | CCPN | discussion, portal, forum, narrative resource, data or information resource, project portal | Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization. | collaborative, computing, project, NMR, software, data, standard, protein, molecule, spectroscopy, global |
is related to: University of Leicester; Leicester; United Kingdom is related to: CCPN Analysis is parent organization of: CCPN Data Model |
Medical Research Council ; Astra-Zeneca ; Genentech ; Dupont Pharma ; GlaxoSmithKline ; BBSRC |
PMID:15613391 | Free for non profit, Public, Acknowledgement requested | https://sourceforge.net/projects/ccpn/ | SCR_016983 | CCPN, Collaborative Computing Project for NMR, The Collaborative Computing Project for NMR | 2026-08-03 09:36:29 | 22 | |||||
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Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility Resource Report Resource Website |
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) | BCF | production service resource, data analysis service, data or information resource, database, access service resource, analysis service resource, service resource, core facility | Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services. | metagenomics, proteomics, protein, structure, functional, genomics, programming, scripting, data | Restricted | SCR_017152 | BCF, Core Facility, University of Oslo, Rikshospitalet-Radiumhospitalet, Bioinformatics | 2026-08-03 09:36:32 | 0 | |||||||||
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MoRDa Resource Report Resource Website 1+ mentions |
MoRDa (RRID:SCR_017278) | software toolkit, software application, database, data processing software, data analysis software, data or information resource, software resource | Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline. | molecular, replacement, protein, structure, data, Xray, crystallography | uses: CCP4 | DOI:10.1107/S2053273315099672 | Restricted | https://ccp4serv7.rc-harwell.ac.uk/ccp4online/ | SCR_017278 | Automatic Molecular Replacement Pipeline | 2026-08-03 09:37:01 | 6 | |||||||
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PatchDock Resource Report Resource Website 50+ mentions |
PatchDock (RRID:SCR_017589) | web service, software application, simulation software, data access protocol, software resource | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-08-03 09:37:05 | 85 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | software resource, data processing software, software application, data analysis software | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-08-03 09:37:13 | 1 | ||||||||
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StatAlign Resource Report Resource Website 1+ mentions |
StatAlign (RRID:SCR_001892) | sequence analysis software, software application, data processing software, data analysis software, software resource | Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java. | software package, bayesian, protein, dna, rna, sequencing, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
PMID:23335014 | Free, Available for download, Freely available | biotools:StatAlign, OMICS_03743 | https://bio.tools/StatAlign | SCR_001892 | StatAlign 2.0 | 2026-08-03 09:31:28 | 1 | ||||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | web service, data access protocol, service resource, software resource | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-08-03 09:31:34 | 2 | ||||
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NEXTDB Resource Report Resource Website 10+ mentions |
NEXTDB (RRID:SCR_004480) | NextDB | production service resource, data analysis service, service resource, database, atlas, analysis service resource, expression atlas, data or information resource | Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae | rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list |
is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: National Institute of Genetics; Shizuoka; Japan |
Core Research for Evolutional Science and Technology ; Japan Science and Technology Corporation ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
Permission required, Acknowledgement required | nlx_46406 | SCR_004480 | Nematode Expression Pattern DataBase | 2026-08-03 09:32:40 | 35 | ||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | data repository, production service resource, service resource, database, source code, storage service resource, analysis service resource, data or information resource, software resource, data set | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-08-03 09:32:40 | 2 | ||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | data repository, production service resource, data analysis service, service resource, database, storage service resource, analysis service resource, data or information resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-08-03 09:32:42 | 118 | |||||
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PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | controlled vocabulary, data or information resource, ontology | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | PRO, Protein Ontology | 2026-08-03 09:32:46 | 0 | |||||||
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Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | data visualization software, software resource, software application, data processing software | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-08-03 09:32:47 | 211 | |||||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | data repository, data or information resource, database, storage service resource, service resource | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-08-03 09:32:50 | 4 | ||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, database, data set | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-08-03 09:32:53 | 135 | ||||
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Synergizer Resource Report Resource Website 1+ mentions |
Synergizer (RRID:SCR_005308) | Synergizer | production service resource, data analysis service, web service, analysis service resource, data access protocol, service resource, software resource | The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access). | gene, protein, json | has parent organization: University of Toronto; Ontario; Canada | nlx_144380 | SCR_005308 | The Synergizer | 2026-08-03 09:32:51 | 9 | ||||||||
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Genetic Testing Registry Resource Report Resource Website 10+ mentions |
Genetic Testing Registry (RRID:SCR_005565) | GTR | data repository, data or information resource, database, storage service resource, service resource | Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. | genetic, gene, clinical, genetic test, condition, phenotype, disease name, trait, drug, protein, analyte, disease, laboratory, molecular, clinical, genetics, people |
lists: MedGen is listed by: OMICtools has parent organization: NCBI |
The community can contribute to this resource | nlx_144654, OMICS_01541 | SCR_005565 | NIH Genetic Testing Registry, GTR: Genetic Testing Registry | 2026-08-03 09:32:43 | 35 | |||||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | production service resource, data analysis service, source code, analysis service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-08-03 09:32:47 | 0 |
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