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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology Resource Report Resource Website 1000+ mentions |
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) | data acquisition software, data or information resource, data processing software, database, software application, software resource | Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013. | function, gene, bioinformatics, data, database, human, meta search engine, prediction, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
biotools:harvester, nif-0000-10169 | https://bio.tools/harvester | SCR_008017 | Harvester IV | 2026-08-29 11:27:55 | 1480 | ||||||||
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HDBase Resource Report Resource Website |
HDBase (RRID:SCR_007132) | HDBase | data or information resource, data set, disease-related portal, portal, topical portal | A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models | drug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathway |
uses: Cytoscape has parent organization: Institute for Systems Biology; Washington; USA |
Huntington''s disease, Control | Hereditary Disease Foundation | nif-0000-00153 | SCR_007132 | HDBase - A Community Website for Huntingtons Disease Research, HDBase - A Community Website for Huntington''s Disease Research | 2026-08-29 11:27:52 | 0 | ||||||
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Ascidian Network for InSitu Expression and Embryological Data Resource Report Resource Website 50+ mentions |
Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) | ANISEED | data or information resource, data repository, database, service resource, software resource, storage service resource |
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website. |
embryology, embryo, gene, genome, anatomy, cis-regulatory, development, morphogenesis, morphology, protein, molecular neuroanatomy resource, cis-regulatory sequence, gene expression, protein annotation, cell, expression profile, function, regulation, blast, visualization, data analysis service, clone, FASEB list | CNRS ; French Ministry of Research ; Marseille-Nice Genopole ; ARC ; European Network QLK3-CT-2001-01890 |
PMID:20647237 | nif-0000-10155 | http://crfb.univ-mrs.fr/aniseed/index.php | SCR_013030 | Aniseed database | 2026-08-29 11:27:39 | 63 | ||||||
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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 | 2026-08-29 11:25:24 | 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 | 2026-08-29 11:25:21 | 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 | 2026-08-29 11:25:30 | 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 | 2026-08-29 11:25:04 | 2043 | ||||||||
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Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-08-29 11:25:06 | 0 | |||||||
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BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | data or information resource, data repository, database, service resource, 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 |
Canadian Institutes for Health Research ; NHGRI U41HG006673; NIDDK K01 DK098285 |
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) | 2026-08-29 11:25:32 | 1378 | ||||||
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mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | 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 | 2026-08-29 11:25:32 | 156 | ||||||||
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Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | 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 | 2026-08-29 11:25:07 | 38 | ||||||||
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REmAb Resource Report Resource Website |
REmAb (RRID:SCR_016239) | analysis service resource, biomaterial analysis service, material analysis service, production service resource, 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 | 2026-08-29 11:25:09 | 0 | ||||||||||
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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 | 2026-08-29 11:25:06 | 0 | ||||||||
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | 2026-08-29 11:25:34 | 4 | |||||||||
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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 | 2026-08-29 11:25:14 | 36 | |||||||||
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ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | 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 | 2026-08-29 11:25:38 | 10 | ||||||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, software resource, web application | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Brain Institute ; Brazilian Council for Research and Technological Development ; Federal University of Rio Grande do Norte ; Multidisciplinary Environment ; NPAD/UFRN |
Free, Freely available | SCR_016506 | 2026-08-29 11:25:47 | 1 | ||||||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-08-29 11:25:18 | 6 | ||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 106370Z14; Wellcome Trust 355804783; Wellcome Trust WT083481; Wellcome Trust WT092340 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-08-29 11:25:16 | 133 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-08-29 11:25:15 | 1 |
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