The Protein-DNA Interface database

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dc.article.number262
dc.catalogadoraba
dc.contributor.authorNorambuena, T.
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.date.accessioned2025-02-06T18:30:58Z
dc.date.available2025-02-06T18:30:58Z
dc.date.issued2010
dc.description.abstractThe Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.
dc.fuente.origenSIPA
dc.identifier.doi10.1186/1471-2105-11-262
dc.identifier.eissn1471-2105
dc.identifier.pubmedid20482798
dc.identifier.pubmedidPMC2885377
dc.identifier.urihttps://doi.org/10.1186/1471-2105-11-262
dc.identifier.urihttps://doi.org/10.1186/1471-2105-11-262
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102165
dc.identifier.wosidWOS:000279730300004
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final12
dc.pagina.inicio1
dc.revistaBMC bioinformatics
dc.rightsacceso abierto
dc.rights.licenseAttribution 2.0 Generic
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/
dc.subjectProtein Data Bank
dc.subjectProtein Data Bank Code
dc.subjectInteraction Class
dc.subjectBiological Unit
dc.subjectProtein Data Bank File
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleThe Protein-DNA Interface database
dc.typeartículo
dc.volumen11
sipa.codpersvinculados82342
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