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FireDB: a compendium of biological and pharmacologically relevant ligands

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dc.contributor.authorMaietta, Paolo
dc.contributor.authorGomez Lopez, Gonzalo
dc.contributor.authorCarro, Angel
dc.contributor.authorPingilley, Benjamin J
dc.contributor.authorLeon, Leticia G
dc.contributor.authorValencia, Alfonso
dc.contributor.authorTress, Michael
dc.contributor.funderMinisterio de Economía y Competitividad (España)
dc.contributor.funderInstituto de Salud Carlos III
dc.contributor.funderUnión Europea
dc.date.accessioned2020-05-06T08:28:38Z
dc.date.available2020-05-06T08:28:38Z
dc.date.issued2014-01
dc.description.abstractFireDB (http://firedb.bioinfo.cnio.es) is a curated inventory of catalytic and biologically relevant small ligand-binding residues culled from the protein structures in the Protein Data Bank. Here we present the important new additions since the publication of FireDB in 2007. The database now contains an extensive list of manually curated biologically relevant compounds. Biologically relevant compounds are informative because of their role in protein function, but they are only a small fraction of the entire ligand set. For the remaining ligands, the FireDB provides cross-references to the annotations from publicly available biological, chemical and pharmacological compound databases. FireDB now has external references for 95% of contacting small ligands, making FireDB a more complete database and providing the scientific community with easy access to the pharmacological annotations of PDB ligands. In addition to the manual curation of ligands, FireDB also provides insights into the biological relevance of individual binding sites. Here, biological relevance is calculated from the multiple sequence alignments of related binding sites that are generated from all-against-all comparison of each FireDB binding site. The database can be accessed by RESTful web services and is available for download via MySQL.es_ES
dc.description.peerreviewedSíes_ES
dc.description.sponsorshipThe Spanish Ministry of Economy and Competitiveness (BIO2012-40205); technical assistance was provided by the Spanish Bioinformatics Institute (INB), a platform of the ISCII; European Union [FP7-REGPOT-2012-CT2012-31637-IMBRAIN to L.G.L.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [grant: BIO2012-40205]es_ES
dc.format.numberDatabase issuees_ES
dc.format.pageD267-72es_ES
dc.format.volume42es_ES
dc.identifier.citationNucleic Acids Res. 2014 Jan;42(Database issue):D267-72.es_ES
dc.identifier.doi10.1093/nar/gkt1127es_ES
dc.identifier.e-issn1362-4962es_ES
dc.identifier.issn0305-1048es_ES
dc.identifier.journalNucleic acids researches_ES
dc.identifier.pubmedID24243844es_ES
dc.identifier.urihttp://hdl.handle.net/20.500.12105/9913
dc.language.isoenges_ES
dc.publisherOxford University Presses_ES
dc.relation.projectIDinfo:eu_repo/grantAgreement/ES/BIO2012-40205)es_ES
dc.relation.projectIDinfo:eu_repo/grantAgreement/ES/FP7-REGPOT-2012-CT2012-31637-IMBRAINes_ES
dc.relation.projectIDinfo:eu_repo/grantAgreement/ES/BIO2012-40205es_ES
dc.relation.publisherversionhttps://doi.org/10.1093/nar/gkt1127es_ES
dc.repisalud.centroISCIII::Centro Nacional de Microbiología
dc.repisalud.institucionCNIOes_ES
dc.repisalud.instituteISCIII
dc.rights.accessRightsopen accesses_ES
dc.rights.licenseAtribución-NoComercial-CompartirIgual 4.0 Internacional*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subject.meshBinding Siteses_ES
dc.subject.meshEvolution, Moleculares_ES
dc.subject.meshInternetes_ES
dc.subject.meshLigandses_ES
dc.subject.meshMolecular Sequence Annotationes_ES
dc.subject.meshPharmaceutical Preparationses_ES
dc.subject.meshProteinses_ES
dc.subject.meshCatalytic Domaines_ES
dc.subject.meshDatabases, Proteines_ES
dc.titleFireDB: a compendium of biological and pharmacologically relevant ligandses_ES
dc.typeresearch articlees_ES
dc.type.hasVersionVoRes_ES
dspace.entity.typePublication
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relation.isAuthorOfPublicationd691c3d3-9e05-4217-a923-08e68ba16baa
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relation.isAuthorOfPublication.latestForDiscoveryfdd2c242-0cf3-45c8-852a-bc29a90bd62a
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