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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | software resource, data analysis software, data processing software, software application, simulation software | 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 | 2026-08-06 09:28:44 | 1146 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, web application, software 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.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
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 | 2026-08-06 09:28:47 | 112 | |||||
|
HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | software resource, data analysis software, data or information resource, data processing software, web application, software application, database | 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 |
National Research Foundation of Korea (NRF) ; Korean government (MEST) 2010-0017649; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Packard Foundations ; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-08-06 09:28:46 | 132 | |||||||||
|
inBio Map Resource Report Resource Website 10+ mentions |
inBio Map (RRID:SCR_016147) | software resource, data or information resource, data processing software, data visualization software, software application, database | 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 | NICHD P01 HD068250; Massachusetts General Hospital ; Broad Institute of MIT and Harvard ; NIMH R01 MH109903; Lundbeck Foundation ; Novo Nordisk Foundation NNF14CC0001 |
PMID:27892958 | Freely available, Free, Available for download | SCR_016147 | inBio | 2026-08-06 09:28:51 | 22 | ||||||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | software resource, alignment software, image analysis software, data processing software, software application | 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 | 2026-08-06 09:28:50 | 3 | ||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, software application, software resource, data processing software | 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) | 2026-08-06 09:28:48 | 15 | |||||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:28:47 | 386 | |||||||
|
Glam2 Resource Report Resource Website 50+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | 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 | 2026-08-06 09:28:45 | 72 | |||||
|
Circular RNA Interactome Resource Report Resource Website 500+ mentions |
Circular RNA Interactome (RRID:SCR_016304) | Circinteractome | web application, software resource | 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 | 2026-08-06 09:28:50 | 666 | |||||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | software resource, web application, data or information resource, data processing software, data visualization software, software application, database | 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 ; NIGMS R01 GM098316; NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-08-06 09:28:51 | 127 | |||||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | software resource, data access protocol, web service, data or information resource, portal | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-08-06 09:28:56 | 15 | ||||||||||
|
OmicsNet Resource Report Resource Website 10+ mentions |
OmicsNet (RRID:SCR_016724) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites). | create, molecular, interaction, network, visually, 3D, gene, protein, microRNA, transcription factor, metabolite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29878180 | Free, Freely available | biotools:omicsnet | https://bio.tools/omicsnet | SCR_016724 | 2026-08-06 09:28:56 | 39 | ||||||
|
Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | sequence analysis software, software resource, image analysis software, alignment software, data access protocol, data analysis software, web service, data processing software, software application | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-08-06 09:28:54 | 0 | |||||||||
|
PMI-Byonic Resource Report Resource Website 10+ mentions |
PMI-Byonic (RRID:SCR_016735) | Byonic | data analysis software, software application, software resource, data processing software | Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type. | Byonic, Protein Metrics Inc., peptide, protein, identification, mass, spectrometry | NIGMS R21 GM085718 | PMID:23255153 | Commercially available | SCR_016735 | Protein Metrics Inc. Byonic, PMI-Byonic, PMI Byonic, Byonic | 2026-08-06 09:28:56 | 22 | |||||||
|
Metascape Resource Report Resource Website 1000+ mentions |
Metascape (RRID:SCR_016620) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies. | analyze, gene, protein, list, data, annotate, resource, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:Metascape | https://bio.tools/Metascape | SCR_016620 | 2026-08-06 09:28:52 | 3483 | ||||||||
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-08-06 09:28:59 | 167 | |||||||||
|
OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | software application, simulation software, software toolkit, software resource | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-08-06 09:28:59 | 1 | |||||||
|
ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data analysis software, software application, software resource, data processing software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-08-06 09:28:55 | 14 | ||||||
|
National Resource for Translational and Developmental Proteomics Resource Report Resource Website |
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) | NRTDP | service resource, training resource, data or information resource, organization portal, portal | Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. | protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis |
has parent organization: Northwestern University; Illinois; USA provides: ProSight Lite |
NIGMS P41 GM108569 | SCR_016907 | The National Resource for Translational and Developmental Proteomics, NRTDP | 2026-08-06 09:28:58 | 0 | ||||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | topical portal, consortium, disease-related portal, data or information resource, organization portal, portal | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-08-06 09:29:01 | 131 |
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