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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers Resource Report Resource Website |
Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers (RRID:SCR_006676) | PRP | data or information resource, portal, registry, topical portal | A guide to peptide-related research and products including custom peptide suppliers, peptide synthesis reagent suppliers that provide resins, coupling reagents, and protected amino acids as well as biologically active peptides and substrates, peptide synthesizers for solution or solid phase peptide synthesis, peptide sequence analysis services, software to calculate the chemical or biochemical properties of peptides, including the prediction of antigenicity or difficult-to-synthesize sequences. There is an additional section on Proteomics Tools for the identification of proteins from peptide sequences determined by mass spectrometry. The site also contains a set of links to educational materials about peptide related research topics. | peptide, training material, modified peptide, library, array, peptide synthesis, protein, peptide sequencing, proteomics | nif-0000-37062 | SCR_006676 | Peptide Resource Page | 2026-09-19 12:51:15 | 0 | |||||||||
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PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Fond der Chemischen Industrie ; German Federal Ministry of Education and Research ; University of Potsdam ; Germany |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/, https://bio.tools/plntfdb | SCR_010899 | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-09-19 12:52:02 | 218 | |||||
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EBIMed Resource Report Resource Website 1+ mentions |
EBIMed (RRID:SCR_005314) | EBIMed | service resource | A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. | protein, gene, annotation, drug, specie, association, database |
is listed by: OMICtools is related to: MEDLINE is related to: PubMed is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: MedlinePlus has parent organization: European Bioinformatics Institute |
OMICS_01180 | SCR_005314 | 2026-09-19 12:50:51 | 1 | |||||||||
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TSRI-Yates Lab Resource Report Resource Website 1+ mentions |
TSRI-Yates Lab (RRID:SCR_005699) | TSRI Yates Lab | data or information resource, laboratory portal, organization portal, portal | Scientists at the Yates Lab at The Scripps Research Institute (TSRI) rely on information yielded by tandem mass spectrometry to identify proteins from complex mixtures. Using this powerful technique, researchers draw upon a cross section of fields to increase the scope, sensitivity, and throughput of technologies for practical proteomics. Biologists provide the questions that drive our research. By identifying complexes that are poorly understood or organism-wide issues requiring further exploration, we gain a theoretical understanding of issues that are tractable only through proteomic strategies. Analytical chemists and biochemists improve our tools for revealing the proteins present in biological samples. Targets for optimization include the isolations used to obtain proteins, the steps to generate peptides from these proteins, and the separation of peptides en route to the mass spectrometer. Chemistry is vital to increasing power of proteomic technology. Computer science yields tools on two scales. First, the sequence corresponding to each peptide''s tandem mass spectrum must be identified. Once those identifications have been completed, additional tools are needed to summarize and organize these identifications. | proteomic, mass spectrometry, protein, peptide | has parent organization: Scripps Research Institute | nlx_149155 | SCR_005699 | Yates Lab at The Scripps Research Institute, The Scripps Research Institute -Yates Lab, TSRI Proteomic Mass Spectrometry Lab, Proteomic Mass Spectrometry Lab at The Scripps Research Institute | 2026-09-19 12:50:58 | 4 | ||||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-09-19 12:50:56 | 37 | ||||||
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PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | data access protocol, software resource, web service | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | PeptideMapper Web-Service, Peptide Mapper | 2026-09-19 12:50:59 | 4 | ||||||
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TOPSAN Resource Report Resource Website 10+ mentions |
TOPSAN (RRID:SCR_005758) | TOPSAN | data or information resource, data repository, database, image collection, service resource, storage service resource | Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation. | protein, structure, 3d, protein structure, protein function, annotate, crowd sourcing, image, annotation, genomics, collaboration |
has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: University of California at San Diego; California; USA |
NIGMS U54 GM074898; NIGMS P20 GM076221 |
PMID:20961957 PMID:20716366 PMID:20944203 PMID:20961957 |
Creative Commons Attribution v3 License, The community can contribute to this resource | nlx_149221 | SCR_005758 | he Open Protein Structure Annotation Network, TOPSAN Project, TOPSAN - The Open Protein Structure Annotation Network | 2026-09-19 12:50:59 | 10 | |||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-09-19 12:50:59 | 20 | ||||||
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ZMM Resource Report Resource Website 10+ mentions |
ZMM (RRID:SCR_005741) | ZMM | data processing software, data visualization software, software application, software resource | ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed. * ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux * ZMM can be used via the command-line interface * ZMM can also be used at Windows via a graphical user interface | molecule, molecular model, peptide, protein, nucleic acid, ligand-receptor complex, small molecule | Commercial license | nlx_149201 | SCR_005741 | ZMM - Molecular Modeling Program | 2026-09-19 12:50:59 | 12 | ||||||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-09-19 12:51:03 | 89 | |||||
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NCBI dbRBC Resource Report Resource Website 1+ mentions |
NCBI dbRBC (RRID:SCR_005959) | dbRBC | data or information resource, database, portal, topical portal | The dbRBC database provides an open, publicly accessible platform for DNA and clinical data related to the human Red Blood Cells (RBC). A new bioinformatics resource, dbRBC, has been installed at the National Center of Biotechnology Information (NCBI). This resource combines the well established Blood Group Antigen Gene Mutation Database (BGMUT) with tools and interlinked resources developed at the NCBI. The main task of dbRBC is to provide access to publicly available genomic, protein and structural information linked to the red blood cell antigens. The site offers a number of resources: * BGMUT Database * Alignment Viewer * SBT Tool * Probe/Primer Resource * Typing Kit Interface * Obstacle | red blood cell, dna, clinical data, allele, anitgen, genome, protein, structure, gold standard |
has parent organization: NCBI has parent organization: Medical University of Graz; Graz; Austria is parent organization of: Blood Group Antigen Gene Mutation Database |
nlx_151317 | SCR_005959 | dbRBC Database | 2026-09-19 12:51:02 | 1 | ||||||||
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MBInfo Resource Report Resource Website 10+ mentions |
MBInfo (RRID:SCR_006768) | MBInfo, MCMF | data or information resource, image collection, portal, topical portal, training resource, video resource | Portal that deals with the process of mechanotransduction, providing in-depth, regularly updated reviews on the mechanics of cellular and molecular function. Each review is written by scientists and subsequently peer reviewed by experts in the field to ensure the content is accurate, reliable and up to date. Each review emphasizes the functional and mechanical aspects of a process, rather than the genetic aspects, with the aim of making this resource accessible to a wider audience. MBInfo is an ideal resource for scientists working in alternative fields, individuals working in industries where products are based on biological principles or students seeking a reliable introduction to a given cellular process. Each topic is written in a pyramid structure. The top of the pyramid is represented by an overview page, providing a basic description of a given function or process. These pages target a broad spectrum of readers and assume only a basic understanding of biology. Further down the pyramid, the reader will encounter the steps involved in the process described and functional modules that address specific mechanical aspects. These pages outline the protein complexes involved and the mechanisms by which they achieve the given process or function. These pages assume the readers have a more in-depth knowledge of scientific terms and principles. For every topic, a series of graphics and/or animations are available. These supplement the reviews, clarify information and guide the reader through complex processes pictorially. This makes MBInfo an ideal teaching resource, whether in the classroom or for clients trying to understand your product. All images and text are copyright protected and are for personal use only. Current Topics include: * Cellular Structures in Mechanosensing and Cell Motility * Methods in the Study of Mechanobiology * Nuclear Mechanotransduction Almost 100 stand alone Glossary Terms are now available. These include short definitions or summaries of proteins and processes that relate to broader topics discussed within the site. Browse an extensive range of figures, tables and videos in our resources section. New quizzes and other interactive content can also be found. | cell, molecule, function, cellular function, molecular function, mechanics, cellular process, mechanobiology, biochemistry, mechanotransduction, review, protein, cellular structure, mechanosensing, cell motility, protein-protein interaction, cytoskeletal system, filopodia, lamellipodium, lamellum, stress fiber, dendritic spine, protein-protein interaction, nucleic acid-protein, small molecule-protein, protein, nucleic acid, small molecule, interaction |
is related to: PSICQUIC Registry is related to: IntAct has parent organization: National University of Singapore; Singapore; Singapore |
Ministry of Education - Singapore ; National Research Foundation - Republic of Singapore |
Acknowledgement requested, Use of images requires consent | nif-0000-06680 | SCR_006768 | MBInfo: A modular approach to cellular functions, Manual of Cellular and Molecular Function | 2026-09-19 12:51:18 | 10 | ||||||
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BAR Resource Report Resource Website 10+ mentions |
BAR (RRID:SCR_006748) | BAR | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available. | gene expression, protein, molecular marker, mapping, tool, genomic, genomics, functional genomics, interaction, molecular interaction, protein-protein interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada |
nlx_152191, biotools:bioanalres_bar | https://bio.tools/bioanalres_bar | SCR_006748 | Bio-Analytic Resource for Plant Biology, Bio-Analytic Resource, Bio-Analytic Resource - the BAR | 2026-09-19 12:51:17 | 48 | ||||||
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ENCODE Resource Report Resource Website 1000+ mentions |
ENCODE (RRID:SCR_006793) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome. | Encyclopedia, DNA, element, functional, human, genome, protein, RNA, level, regulatory, gene, active, disease, analysis |
uses: Segway - a way to segment the genome is used by: BioSample Database at EBI is used by: VizHub is used by: GEMINI is used by: Deep Blue Epigenomic Data Server is recommended by: National Library of Medicine is listed by: OMICtools is affiliated with: GENCODE is related to: Factorbook is related to: UCSC Genome Browser is related to: modENCODE is related to: UCSC Genome Browser is related to: Encode is related to: Broad Institute Genomics Platform has parent organization: University of California at Santa Cruz; California; USA |
NHGRI | PMID:21526222 | Free, Freely available | nif-0000-02797, r3d100013051, SCR_017493, OMICS_00532 | http://encodeproject.org/ENCODE/, https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements, https://www.encodeproject.org/, https://doi.org/10.17616/R31NJMKB | SCR_006793 | ENCODE - Encyclopedia of DNA Elements, ENCODE + Epigenomics Roadmap Combined Data Browser, Encyclopedia of DNA Elements, Encyclopedia of DNA Elements (ENCODE) | 2026-09-19 12:51:18 | 4206 | |||||
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CD-HIT-OTU Resource Report Resource Website 50+ mentions |
CD-HIT-OTU (RRID:SCR_006983) | CD-HIT-OTU | software resource | Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12). | 454, read, illumina, rrna, fasta, metagenome, sequence, clustering, metagenomics, next-generation sequencing, protein |
is listed by: OMICtools has parent organization: CD-HIT |
PMID:22772836 PMID:21899761 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01441 | SCR_006983 | 2026-09-19 12:51:22 | 89 | |||||||
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Array Information Library Universal Navigator Resource Report Resource Website 1+ mentions |
Array Information Library Universal Navigator (RRID:SCR_006967) | AILUN | analysis service resource, data analysis service, data or information resource, database, production service resource, resource, service resource | Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species. | gene expression, gene, array, clone, probe, protein, proteomic, annotation, analytical service, probe id, comparison, microarray, probe sequence, gene identifier, annotation file, web service |
is related to: Gene Expression Omnibus is related to: Entrez Gene has parent organization: Stanford University School of Medicine; California; USA |
Lucile Packard Foundation for Childrens Health ; Howard Hughes Medical Institute ; Pharmaceutical Research and Manufacturers of America Foundation ; NLM K22 LM008261; NIDDK R01GM079719 |
PMID:17971777 | nif-0000-33004 | SCR_006967 | 2026-09-19 12:51:22 | 5 | |||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-09-19 12:51:22 | 6 | |||||
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IntAct Resource Report Resource Website 1000+ mentions |
IntAct (RRID:SCR_006944) | IntAct | data or information resource, data repository, database, service resource, storage service resource | Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available. | protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standard |
is used by: ChannelPedia is used by: MINT is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: 3D-Interologs is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: VirHostNet: Virus-Host Network is related to: PSICQUIC Registry is related to: UniProt is related to: SIB Swiss Institute of Bioinformatics is related to: I2D is related to: InnateDB is related to: MatrixDB is related to: MBInfo is related to: AgBase is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PSI-MI is related to: Agile Protein Interactomes DataServer has parent organization: European Bioinformatics Institute works with: IMEx - The International Molecular Exchange Consortium |
European Union contract FP7-HEALTH-2007-223411; European Union contract FP7-HEALTH-2007-200767 |
PMID:24234451 PMID:22121220 PMID:19850723 PMID:17145710 PMID:14681455 |
Apache License, v2, (software), Creative Commons Attribution License, (data), The community can contribute to this resource | OMICS_01918, r3d100010671, nif-0000-03026 | https://doi.org/10.17616/R3QS4R | SCR_006944 | IntAct | 2026-09-19 12:51:21 | 1955 | ||||
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PrimerBank Resource Report Resource Website 1000+ mentions |
PrimerBank (RRID:SCR_006898) | PrimerBank | data or information resource, data repository, database, service resource, storage service resource | Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd. | electrophoresis, gene expression, quantitative pcr, gel, gene, agarose, algorithm, amplification, human, molecular probe, primer database, mouse, pcr, primer, primer pair, protein, quantification, reaction, secondary structure, polymerase chain reaction, real-time pcr, pcr primer, detection, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U01 HL66678 | PMID:22086960 PMID:19906719 PMID:19108745 PMID:14654707 |
Public, Acknowledgement requested, The community can contribute to this resource | nif-0000-21333, OMICS_02323, biotools:primerbank | https://bio.tools/primerbank | SCR_006898 | PrimerBank: PCR Primers for Gene Expression Detection and Quantification | 2026-09-19 12:51:20 | 1709 | ||||
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YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-09-19 12:51:20 | 34 |
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