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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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STOP Resource Report Resource Website 100+ mentions |
STOP (RRID:SCR_005322) | STOP | analysis service resource, data analysis service, production service resource, service resource | STOP is a multi-ontology enrichment analysis tool. It is intended to be used to help from hypothesis about large sets of genes or proteins. The annoations used for enrichment analysis are obtained automatically applying text descriptions of genes and proteins to the NCBO annotator. Text for genes is found using NCBI entrez gene, and text for proteins is found using UniProt. The text is then run though NCBO annotator with all the available ontologies. For more information about the NCBO annotator please visit: http://bioportal.bioontology.org/ The goal of National Center for Biomedical Ontology (NCBO) is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. This work is an expansion of the work of Rob Tirrell and others on RANSUM This probject would not be possible without the contributions of Emily Howe, Uday Evani, Corey Powell, Mathew Fleisch, Tobias Wittkop, Ari Berman, Nigam Shah and Sean Mooney An account is required. | gene ontology, resource:go, gene, protein, annotation |
is related to: Entrez Gene is related to: UniProt is related to: NCBO Annotator has parent organization: Buck Institute; California; USA has parent organization: Stanford University; Stanford; California |
nlx_144382 | SCR_005322 | Statistical Tracking of Ontological Phrases, Statistical Tracking of Ontological Phrases (STOP) | 2026-09-12 01:01:37 | 458 | ||||||||
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GORetriever Resource Report Resource Website 10+ mentions |
GORetriever (RRID:SCR_005633) | GORetriever | analysis service resource, data analysis service, production service resource, service resource | GORetriever is used to find all of the GO annotations corresponding to a list of user-supplied protein identifiers. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. Platform: Online tool | gene, annotation, protein, ontology or annotation search engine |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149140 | SCR_005633 | AgBase GORetriever | 2026-09-12 01:01:38 | 13 | |||||
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STRING Resource Report Resource Website 10000+ mentions |
STRING (RRID:SCR_005223) | STRING | data or information resource, database | Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013) | protein association, protein functional association, protein interaction, protein-protein interaction, protein, sequence, protein sequence, interaction, gene, FASEB list |
is used by: MobiDB is used by: PAXdb is listed by: Nuclear Receptor Signaling Atlas is listed by: NIDDK Information Network (dkNET) is related to: Biomine is related to: PSICQUIC Registry is related to: ShinyGO has parent organization: European Molecular Biology Laboratory has plug in: Cytoscape StringApp |
BMBF ; European Union FP6 ; EMBO ; ProBioC ; Swiss Institute of Bioinformatics |
PMID:23203871 PMID:21045058 PMID:18940858 PMID:17098935 PMID:15608232 PMID:12519996 |
nif-0000-03503, r3d100010604 | https://doi.org/10.17616/R3VS40 | SCR_005223 | Search Tool for the Retrieval of Interacting Genes/Proteins, STRING - Known and Predicted Protein-Protein Interactions | 2026-09-12 01:01:36 | 32678 | |||||
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Moffitt Cancer Center Proteomics and Metabolomics Core Facility Resource Report Resource Website |
Moffitt Cancer Center Proteomics and Metabolomics Core Facility (RRID:SCR_012168) | access service resource, core facility, service resource | Provides instrumentation for proteomics and metabolomics studies, including protein, peptide and metabolite separations, MS instrumentation for protein, peptide and metabolite analysis, and data systems, software, and bioinformatics tools for data archiving and analysis. Proteomics Core performs routine analytical proteomics services, including target discovery, identification and quantitation, and also provides platforms for functional proteomics using variety of strategies for protein separation, sub-proteome enrichment, post-translational modification analysis, and quantitation. | protein, peptide and metabolite separations, peptide and metabolite analysis, data systems, |
is listed by: ScienceExchange is listed by: ABRF CoreMarketplace has parent organization: Moffitt Cancer Center |
SciEx_10069, ABRF_2761 | https://coremarketplace.org/?FacilityID=2761&citation=1 | http://www.scienceexchange.com/facilities/proteomics-core-facility-moffitt | SCR_012168 | H. Lee Moffitt Cancer Center and Research Institute Proteomics and Metabolomics Core Facility, Moffitt Proteomics Core Facility | 2026-09-12 01:03:37 | 0 | |||||||
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CGDB Resource Report Resource Website 10+ mentions |
CGDB (RRID:SCR_011959) | CGDB | data or information resource, data set | A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. | protein, image, coarse-grained, molecular dynamics, membrane protein |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC | PMID:18937097 PMID:18208379 |
Acknowledgement requested | OMICS_01608 | SCR_011959 | Coarse Grained Database, Coarse-Grained Database, CG Database | 2026-09-12 01:03:37 | 32 | |||||
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McGill Cell Imaging and Analysis Network Core Facility Resource Report Resource Website 1+ mentions |
McGill Cell Imaging and Analysis Network Core Facility (RRID:SCR_012623) | McGill CIAN | access service resource, core facility, service resource | Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training. | Light, microscopy, image, analysis, service, automation, high, throughput, screening, protein, expression, antibody, production, training |
is listed by: ScienceExchange is related to: McGill University Labs and Facilities has parent organization: McGill University; Montreal; Canada |
Restricted | SciEx_569 | http://www.scienceexchange.com/facilities/cell-imaging-and-analysis-network-cian | SCR_012623 | McGill University Cell Imaging and Analysis Network, McGill Cell Imaging and Analysis Network (CIAN), McGill University Cell Imaging and Analysis Network (CIAN) | 2026-09-12 01:03:44 | 1 | ||||||
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Glyco-CD Resource Report Resource Website |
Glyco-CD (RRID:SCR_001574) | GlycoCD, | data or information resource, data set | Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology. | carbohydrate, glycobiology, glycan, lectin, antigen, interaction, protein, cell surface molecule, microarray, carbohydrate recognition, cluster of differentiation, oligosaccharide sequence, glycoprotein, glycosphingolipid, carbohydrate recognition site, leukocyte, antibody, endothelial cell, epithelial cell | has parent organization: glycosciences.de | European Union FP7/2007-2013 215536 | PMID:22847935 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152887 | http://www.glycosciences.de//Glyco-CD/ | SCR_001574 | GlycoCD database, Glyco-CD databank, Glyco-CD database | 2026-09-12 01:03:12 | 0 | ||||
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Novus Biologicals Resource Report Resource Website 10000+ mentions |
Novus Biologicals (RRID:SCR_004286) | commercial organization | Commercial antibody vendor which supplies antibodies and other products to life science researchers. | primary antibody, secondary antibody, antibody pair, antibody pack, lysate, peptide, protein, rnai, kit, slide, isotype control, database, IMGENEX, FASEB list | is related to: Antibody Registry | grid.420893.4, Wikidata: Q7065122, nlx_152382, nlx_143665, ISNI: 0000 0004 0627 4379 | https://ror.org/021q72e63 | SCR_004286 | Novus, Novus Biologics LLC | 2026-09-12 01:03:14 | 23749 | ||||||||
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National Natural Toxins Research Center Resource Report Resource Website 10+ mentions |
National Natural Toxins Research Center (RRID:SCR_002824) | VRC, NNTRC | access service resource, core facility, service resource | Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville. | venom, venomous snake, snake, LD50, ED50, toxin, toxins, electrophoretic titration, enzyme, fibrinolytic, function, assay, cancer, cell, chromatography, compound, disintegrin, venom gland, hemorrhagic, integrin, metalloproteinases, polypeptide, protein, proteolytic, species, vendor, research training |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Texas A and M University-Kingsville; Texas; USA |
NIH Office of the Director P40 OD010960 | Free, Freely available | nif-0000-24966 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | http://ntrc.tamuk.edu/, https://www.tamuk.edu/artsci/departments/nntrc/index.html | SCR_002824 | Viper Resource Center | 2026-09-12 01:03:13 | 35 | ||||
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UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-09-12 01:03:16 | 0 | |||||||||
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National Resource for the Mass Spectrometric Analysis of Biological Macromolecules Resource Report Resource Website |
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) | National Resource for the Mass Spectrometric Analysis of Biological Macromolecules | biomedical technology research center, training resource | Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available. | systems biology technology center, mass spectrometric, analysis, peptide, protein, software, proteomic, cellular function | has parent organization: Rockefeller University; New York; USA | NIGMS | nlx_152683 | SCR_009007 | 2026-09-12 01:03:18 | 0 | ||||||||
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CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-09-12 01:03:18 | 5 | |||||
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UCSD Center for NMR Spectroscopy and Imaging of Proteins Resource Report Resource Website |
UCSD Center for NMR Spectroscopy and Imaging of Proteins (RRID:SCR_001401) | NMR Resource at UCSD | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops new technology for NMR spectroscopy and makes it available to the biomedical research community for structure determination of proteins in biological supramolecular assemblies, such as membrane proteins or virus particles. The principal applications are to membrane-associated proteins; however, the approach is generally applicable to polypeptides that cannot be prepared in forms suitable for X-ray crystallography or multidimensional solution NMR spectroscopy. As a result, there are also applications to viruses and other biological systems. The principal instrumentation consists of high-field NMR spectrometers dedicated to high-resolution solid-state NMR spectroscopy. The spectrometers are capable of the full-range of multiple-resonance experiments on stationary and spinning samples; however, the major emphasis is on methods that utilize mechanically or magnetically oriented samples. Development encompasses preparation of samples, including: * Expression and purification of membrane proteins * Design and construction of instrumentation, especially probes * Implementation of new pulse sequences and other experimental protocols for solid-state NMR spectroscopy * Calculations for the processing of experimental data and protein structure determination from the orientational constraints derived from these data | nmr spectroscopy, structure, protein, nmr spectrometer, expression, purification, membrane protein, probe, pulse sequence, virus particle | has parent organization: University of California at San Diego; California; USA | NIBIB P41EB002031 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152626 | SCR_001401 | Center for NMR Spectroscopy and Imaging of Proteins, Resource for NMR Molecular Imaging of Proteins | 2026-09-12 01:03:11 | 0 | ||||||
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GeneWays Resource Report Resource Website |
GeneWays (RRID:SCR_000572) | Geneways | service resource | System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. | pathway, molecule, literature, natural language processing, gene, protein, interaction, database |
is listed by: OMICtools has parent organization: Argonne National Laboratory has parent organization: Columbia University; New York; USA |
DOE ; NIGMS GM61372; NSF |
PMID:15016385 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30019, SCR_008368, OMICS_01182 | http://anya.igsb.anl.gov/genewaysApp | SCR_000572 | GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data | 2026-09-12 01:03:10 | 0 | ||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-12 01:02:53 | 6 | ||||
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Batch Entrez Resource Report Resource Website 50+ mentions |
Batch Entrez (RRID:SCR_016634) | software application, software resource | Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers. | load, number, genome, record, retrieval, nucleotide, sequence, protein, batch, mode |
has parent organization: NCBI works with: Entrez |
Public, Free, Freely available | SCR_016634 | 2026-09-12 01:02:54 | 60 | ||||||||||
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Aline Resource Report Resource Website 1+ mentions |
Aline (RRID:SCR_016886) | software application, software resource | Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures. | protein, sequence, alignment, editor, publication, quality, alter, embellish, markup, biochemistry, bioinformatics |
is related to: University of Dundee; Scotland; United Kingdom is related to: University of Western Australia; Perth; Australia |
PMID:19390156 | Free, Available for download, Freely available | SCR_016886 | 2026-09-12 01:02:54 | 2 | |||||||||
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DOMAINATRIX Resource Report Resource Website |
DOMAINATRIX (RRID:SCR_016084) | software application, software resource | Software for protein domain search. It is a part of Embassy software package. | protein, domain, search, molecular, biology | is listed by: Debian | Free, Available for download, Freely available | http://emboss.sourceforge.net/what/, https://sources.debian.org/src/embassy-domainatrix/ | SCR_016084 | Embassy-domainatrix | 2026-09-12 01:02:53 | 0 | ||||||||
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Concavity Resource Report Resource Website 50+ mentions |
Concavity (RRID:SCR_016063) | software application, software resource, software toolkit | Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets. | predict, protein, ligand, binding, site, catalytic, drug, algorithm |
is listed by: Debian is listed by: OMICtools is related to: Princeton University; New Jersey; USA |
PMID:19997483 DOI:10.1371/journal.pcbi.1000585 |
Free, Available for download | OMICS_04161 | http://manpages.ubuntu.com/manpages/bionic/man1/concavity.1.html, https://sources.debian.org/src/concavity/ | SCR_016063 | 2026-09-12 01:02:53 | 94 | |||||||
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Conservation Resource Report Resource Website 1000+ mentions |
Conservation (RRID:SCR_016064) | software application, software resource, software toolkit | Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands. | scoring, protein, sequence, conservation, Jensen-Shannon, divergence, predict, catalytic, site, bound, ligands, clustal, fasta, concave | is related to: Princeton University; New Jersey; USA | NIGMS GM076275; NIH P50 GM071508; NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-09-12 01:02:53 | 1606 |
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