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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 |
University of Potsdam ; Germany ; German Federal Ministry of Education and Research ; Fond der Chemischen Industrie |
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 | 2026-02-16 09:47:59 | 201 | |||||
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mGOASVM Resource Report Resource Website 1+ mentions |
mGOASVM (RRID:SCR_013098) | mGOASVM | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available. | subcellular localization, gram-negative protein, virus, protein |
is listed by: OMICtools has parent organization: Hong Kong Polytechnic University; Hong Kong; China |
PMID:23130999 | OMICS_01627 | SCR_013098 | 2026-02-16 09:48:24 | 4 | ||||||||
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PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | software application, data processing software, data analysis software, software resource, simulation software | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-02-16 09:48:26 | 4151 | |||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | web service, data analysis service, analysis service resource, data access protocol, software resource, source code, production service resource, service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/ https://bio.tools/sift https://sources.debian.org/src/sift/ |
http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-02-16 09:48:13 | 10223 | |||
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Drug ADME Associated Protein Database Resource Report Resource Website 1+ mentions |
Drug ADME Associated Protein Database (RRID:SCR_013501) | data repository, database, storage service resource, service resource, data or information resource | A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion (ADME) associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Associated references are also included. Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates. ADME Class Based on their respective role of pharmacokinetics, ADME-associated proteins can be classified into four categories: A: This Category includes proteins involved in the absorption or re-absorption of drugs into systemic system. D: This category includes proteins responsible for facilitating the distribution of drugs from the systemic system to the target sites or away from the target sites back to the systemic system. Certain plasma proteins and intracellular binding proteins may alter free drug concentration by acting as drug storage depot. These proteins thus play a regulatory role in drug distribution and they are thus included in Category D. Based on their role in drug distribution, proteins in this category can be further divided into three groups D1, D2, and D3. The first group D1 includes transporters capable of transporting chemicals across membranes of various tissue barriers from the systemic system into the target sites. Blood-brain barrier and placenta barrier are examples of tissue barrier. Proteins in the second group D2 are responsible for transporting drugs back into the systemic system. Proteins in the third group D3 mainly function as drug storage depot. These include ligand binding proteins in plasma and intracellular proteins. M: Proteins in category M are drug-metabolizing enzymes. These enzymes can be further divided into two separate groups M1 and M2, according to whether the corresponding enzymatic reaction is phase I or phase II. E: This category E includes proteins that enable the excretion or presystemic elimination of drugs. Some proteins belong to more than one category: e.g. P-glycoprotein both limits intestinal absorption and excludes drugs from the brain back to the blood. It thus belongs to both Category E and D. For those proteins capable of transporting natural substrates without literature report of interaction with a drug, a postfix potential is attached to their respective classification to indicate that their specific role in ADME is yet to be confirmed. Use of ADME-AP for commercial purposes is not allowed. | drug, drug-metabolizing enzymes, elimination, excretion, functions, absorption, distribution, intracellular proteins, ligand binding proteins, ligands, metabolism, pharmacokinetics, protein, similarities, substrates, targets, tissue distributions, transporters | has parent organization: National University of Singapore; Singapore; Singapore | nif-0000-21131 | SCR_013501 | ADMEAP | 2026-02-16 09:48:23 | 3 | |||||||||
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Protein Subcellular Location Image Database Resource Report Resource Website |
Protein Subcellular Location Image Database (RRID:SCR_008663) | PSLID | data set, image analysis service, data repository, database, storage service resource, service resource, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging. |
protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, subcellular localization, 3d spatial image, 2d spatial image, micrograph, content-based retrieval, green fluorescent protein |
is listed by: 3DVC is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Merck Company Foundation ; NIGMS GM075205; NCI R33 CA83219; NSF MCB-8920118 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33313 | SCR_008663 | PSLID - Protein Subcellular Location Image Database, Protein Subcellular Location Image Database | 2026-02-16 09:47:14 | 0 | ||||||
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Molecular Libraries Program Resource Report Resource Website 10+ mentions |
Molecular Libraries Program (RRID:SCR_008847) | MLP | organization portal, analysis service resource, material analysis service, topical portal, portal, production service resource, service resource, data or information resource | High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem''''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site. | molecule, compound, probe, small molecule, high throughput screening, gene, cell, biochemical pathway, drug development, protein, pathway |
is used by: LINCS Information Framework is related to: BARD is related to: NIH Clinical Collection is related to: PubChem has parent organization: National Institutes of Health |
NIH | nlx_146246 | SCR_008847 | Molecular Libraries, Molecular Libraries Initiative | 2026-02-16 09:47:17 | 15 | |||||||
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Quertle: Relationship-Driven Biomedical Search Resource Report Resource Website |
Quertle: Relationship-Driven Biomedical Search (RRID:SCR_008676) | research forum portal, database, topical portal, portal, data or information resource, disease-related portal | Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. Quertle''s friendly interface makes it simple to search and refine results. Using advanced semantics, Quertle finds quality results, not just long lists. And it hods: all of PubMed, a growing number of full-text documents, news, and more. Features: :- Find Relationships, not Just :- Focus on Core Concepts: Since Quertle searches for Relationships, all the terms in your query must be found together in a meaningful way. Thus, Quertle immediately gives you results with more relevance. :- Unleash the Strength of Power Terms: Use Power Terms to search for categories of objects. For instance, you can use Protein to search for any protein, rather than the occurrence of the term, protein. View all Power Terms. :- Search Full-text Documents: The Quertle search engine has been optimized to search full-text documents, including the Material and Methods section (but not the Bibliography). :- Use Real Biology & Chemistry Terms: Quertle recognizes capital TWIST as the transcription factor (not the verb), and capital NO as nitrous oxide(not a negative). So, use proper capitalization in your query, and you won''t be lost in a sea of irrelevant results. :- Look for the Quertle Difference on the Results Page : More relevant results : Easy filtering and breadcrumb tracking : Automatic identification of key concepts : Single-click access to PDFs of full-text documents :Keyword: Biomedical, Search engine, Database, Researcher, Linguistic, Technology, Semantic, Relationship, Protein, Biology, Chemistry, : | all the terms in your query must be found together in a meaningful way. thus, biology, chemistry, chemistry terms: quertle recognizes capital twist as the transcription factor (not the verb), database, if you search for two or more terms, including the material and methods section (but not the bibliography). - use real biology &, linguistic, not just the terms scattered within the same document. - focus on core concepts: since quertle searches for relationships, protein, quertle immediately gives you results with more relevance. - unleash the strength of power terms: use power terms to search for categories of objects. for instance, rather than the occurrence of the term, relationship, researcher, search engine, semantic, technology, use proper capitalization in your query, you can use protein to search for any protein, you will find occurrences of a conceptual relationship | nif-0000-33690 | SCR_008676 | Quertle | 2026-02-16 09:47:14 | 0 | ||||||||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | software application, data analysis service, analysis service resource, software resource, production service resource, service resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-02-16 09:47:19 | 601 | |||||
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PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-02-16 09:47:41 | 1688 | |||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | data repository, database, storage service resource, service resource, data or information resource | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-02-16 09:47:40 | 0 | ||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | software application, text-mining software, database, software resource, data or information resource | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-02-16 09:47:46 | 18 | |||||||||
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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 | 2026-02-16 09:46:41 | 4 | ||||||
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TOPSAN Resource Report Resource Website 10+ mentions |
TOPSAN (RRID:SCR_005758) | TOPSAN | image collection, data repository, database, storage service resource, service resource, data or information 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 | 2026-02-16 09:46:32 | 10 | |||||
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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 | 2026-02-16 09:46:31 | 4 | ||||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | 2026-02-16 09:46:41 | 20 | ||||||
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ZMM Resource Report Resource Website 10+ mentions |
ZMM (RRID:SCR_005741) | ZMM | software application, data processing software, data visualization software, 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 | 2026-02-16 09:46:32 | 12 | ||||||||
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UMD-BRCA1/ BRCA2 databases Resource Report Resource Website 10+ mentions |
UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) | UMD-BRCA1/ BRCA2 databases | data repository, database, storage service resource, service resource, data or information resource | The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau. | cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, woman, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Health and Medical Research; Rennes; France |
Breast cancer, Ovarian cancer | French National Cancer Institute ; European Union FP7/2007-2013; Association dAide a la Recherche Cancerologique de Saint Cloud |
PMID:22144684 | The UMD- BRCA1 Locus Specific Databases constitute the intellectual property of the curators of the database. Any unauthorized copying, Storage or distribution of this material without written permission from the curators would lead to copyright infringement with possible ensuing litigation. | nlx_151608, biotools:brca_share | https://bio.tools/brca_share | SCR_006128 | UMD-BRCA1 mutations database, UMD-BRCA1 / BRCA2 databases, UMD-BRCA1/BRCA2 databases | 2026-02-16 09:46:43 | 26 | |||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | 2026-02-16 09:46:36 | 77 | |||||
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NCBI dbRBC Resource Report Resource Website 1+ mentions |
NCBI dbRBC (RRID:SCR_005959) | dbRBC | database, data or information resource, topical portal, 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 | 2026-02-16 09:46:42 | 1 |
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