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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
PfamResource, data or information resource, databaseA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).database, clan, structure, sequence, protein family, domainSCR_004726(Pfam, RRID:SCR_004726)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL core funds, Howard Hughes Medical Institute, Wellcome Trustrelated to: Conserved Domain Database, Monarch Initiative, SUPFAM, DBD: Transcription factor prediction database, DOMINE: Database of Protein Interactions, GeneSpeed- A Database of Unigene Domain Organization , Eukaryotic Linear Motif, TopoSNP, GOTaxExplorer, TrED, ProOpDB, Algal Functional Annotation Tool, used by: Mutation Annotation and Genomic Interpretation, MobiDB, listed by: OMICtoolsReferences (2)Last checked downnlx_72111, OMICS_01696http://pfam.sanger.ac.uk/
SHERPA RoMEOResource, database, data or information resourceA database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit.database, publisher policy, open accessSCR_013815(SHERPA RoMEO, RRID:SCR_013815)University of Nottingham; Nottingham; United Kingdom JISC, Wellcome Trustrelated to: Connected Researchers, listed by: Connected ResearchersLast checked up
ChEMBLResource, data or information resource, databaseCollection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.database, compound, data, bioassay, bioactive, molecule, drug, discoverySCR_014042(ChEMBL, RRID:SCR_014042)EMBL Member States, EU Innovative Medicines Initiative, GSK, Medicines for Malaria Ventures, Pfizer, Syngenta, Wellcome Trustused by: GEROprotectors, PubChemPMID:21948594Last checked up
EnsemblResource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resourceCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, dataSCR_002344(Ensembl, RRID:SCR_002344)European Bioinformatics Institute , Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL, European Union, FP6, FP7, MRC, NHGRI, Wellcome Trustrelated to: Ensembl Genomes, GermOnline, CandiSNPer, Human Splicing Finder, NGS-SNP, Sanger Mouse Resources Portal, DECIPHER, Ensembl Genomes, PeptideAtlas, AnimalTFDB, Bgee: a dataBase for Gene Expression Evolution, FlyMine, Rat Gene Symbol Tracker, UniParc at the EBI, go-db-perl, UniParc, G:Profiler, RIKEN integrated database of mammals, VBASE2, p300db, used by: NIF Data Federation, Animal QTLdb, Monarch Initiative, ChannelPedia, Blueprint Epigenome, HmtPhenome, listed by: OMICtools, Biositemaps, re3data.org, LabWorm, works_with: Genotate, CellPhoneDB, Open Regulatory Annotation DatabaseReferences (2)Last checked upnif-0000-21145, OMICS_01647
PANDIT : Protein and Associated Nucleotide Domains with Inferred TreesResource, data or information resource, databasePANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.gold standard, database, protein, associated nucleotide domainSCR_003321(PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees, RRID:SCR_003321)European Bioinformatics Institute Wellcome TrustReferences (2)Last checked upnif-0000-03241
European Bioinformatics InstituteOrganization, organization portal, portal, data or information resourceNon-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, proteinSCR_004727(European Bioinformatics Institute, RRID:SCR_004727)European Molecular Biology Laboratory BBSRC, EMBL member states, European Union, Industry Programme partners, NIH, UK Research Councils, Wellcome Trustrelated to: AgedBrainSYSBIO, ProteomeXchange, Open PHACTS, RHEA, TraCeR, used by: Blueprint Epigenome, listed by: re3data.orgLast checked upnlx_72386
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