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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data or information resource, data repository, data set, service resource, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-09-12 12:58:59 | 37 | |||||||
|
HPEPDOCK Server Resource Report Resource Website 50+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
Huazhong University of Science and Technology ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-09-12 12:59:02 | 73 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-09-12 12:59:02 | 316 | |||||||
|
ToxinPred Resource Report Resource Website 100+ mentions |
ToxinPred (RRID:SCR_018542) | analysis service resource, production service resource, service resource, software resource, software toolkit | Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins. | Toxin, toxicity, toxicity prediction, peptide toxicity prediction, peptide design, protein, peptide mutation, toxic region, protein toxic region | Council of Scientific and Industrial Research Govt. of India ; Department of Biotechnology Govt. of India |
PMID:29300301 | Free, Freely available | SCR_018542 | 2026-09-12 12:59:02 | 244 | |||||||||
|
ProteinPilot Software Resource Report Resource Website 1000+ mentions |
ProteinPilot Software (RRID:SCR_018681) | data analysis software, data processing software, software application, software resource | Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems. | Protein identification, protein expression, protein expression analysis, protein, post translational modification, proteomics, mass spectrometry system | Restricted | SCR_018681 | Protein Pilot, Protein Pilot Software | 2026-09-12 12:59:04 | 1489 | ||||||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-09-12 12:59:04 | 0 | ||||||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-09-12 12:58:33 | 1261 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; INBIOMED initiative ; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; University of Vigo 09VIB10 to F.F-.R.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-09-12 12:58:33 | 125 | |||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-09-12 12:58:34 | 489 | |||||||
|
HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes. | probability, gene, protein, encode, statistic, likelihood, network, bayesian, omic, pathway, guilt by association, FASEB list |
has parent organization: University of Texas at Austin; Texas; USA has parent organization: Yonsei University; Seoul; South Korea |
Korean government (MEST) 2010-0017649; National Research Foundation of Korea (NRF) ; Packard Foundations ; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-09-12 12:58:35 | 135 | |||||||||
|
inBio Map Resource Report Resource Website 10+ mentions |
inBio Map (RRID:SCR_016147) | data or information resource, data processing software, data visualization software, database, software application, software resource | Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research. | ppi, protein, visualization | Broad Institute of MIT and Harvard ; Lundbeck Foundation ; Massachusetts General Hospital ; NICHD P01 HD068250; NIMH R01 MH109903; Novo Nordisk Foundation NNF14CC0001 |
PMID:27892958 | Freely available, Free, Available for download | SCR_016147 | inBio | 2026-09-12 12:58:35 | 23 | ||||||||
|
MultiNet Resource Report Resource Website 10+ mentions |
MultiNet (RRID:SCR_016149) | software resource | Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network. | network, integration, human, protein, interactome, gene, interaction | PMID:23505346 | Free, Available for download | SCR_016149 | 2026-09-12 12:58:36 | 14 | ||||||||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | alignment software, data processing software, image analysis software, software application, software resource | Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned. | multiple, sequence, alignment, algorithm, distance, approach, homologous, protein, DNA, RNA, acurate, fast |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:19478997 | Free, available for download | https://sources.debian.org/src/fsa/ | SCR_016114 | Fast Statistical Alignment, FSA: Fast Statistical Alignment | 2026-09-12 12:58:35 | 3 | ||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, data processing software, software application, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-09-12 12:58:35 | 19 | |||||||
|
Glam2 Resource Report Resource Website 100+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-09-12 12:58:35 | 203 | |||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-09-12 12:58:36 | 142 | |||||||||
|
Circular RNA Interactome Resource Report Resource Website 500+ mentions |
Circular RNA Interactome (RRID:SCR_016304) | Circinteractome | software resource, web application | Web tool for exploring circular RNAs and their interacting proteins and microRNAs. Predicts the miRNAs which can potentially target the circRNA. | exploring, circular, RNA, miRNA, interacting, protein, predict, target, circRNA | the National Institute on Aging Intramural Research Program of the National Institutes of Health | PMID:26669964 | Free, Freely available, Available for download | SCR_016304 | Circular interactome | 2026-09-12 12:58:37 | 783 | |||||||
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Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-09-12 01:01:25 | 1 | |||||
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HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-09-12 01:01:27 | 2 | |||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-09-12 01:01:27 | 459 |
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