PDIviz: analysis and visualization of protein-DNA binding interfaces

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dc.catalogadoraba
dc.contributor.authorRibeiro J.
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.contributor.authorSchüller, Andreas
dc.date.accessioned2025-02-06T18:54:43Z
dc.date.available2025-02-06T18:54:43Z
dc.date.issued2015
dc.description.abstractSummary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction. Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.
dc.format.extent3 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1093/bioinformatics/btv203
dc.identifier.eissn1460-2059
dc.identifier.issn1367-4803
dc.identifier.scopusid2-s2.0-84939520208
dc.identifier.urihttps://doi.org/10.1093/bioinformatics/btv203
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102169
dc.identifier.wosidWOS:000359666600023
dc.information.autorucFacultad de Ciencias Biológicas; Schüller, Andreas; 0000-0002-4443-4279; 207692
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.issue.numero16
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final2753
dc.pagina.inicio2751
dc.revistaBIOINFORMATICS
dc.rightsacceso abierto
dc.rights.licenseAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titlePDIviz: analysis and visualization of protein-DNA binding interfaces
dc.typeartículo
dc.volumen31
sipa.codpersvinculados207692
sipa.codpersvinculados82342
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