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GPU-Based De- tection of Protein Cavities using Gaussian Surfaces

2017Journal article Open access
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dc.contributor.authorDias, Sérgio
dc.contributor.authorMartins, Ana Mafalda
dc.contributor.authorNguyen, Quoc
dc.contributor.authorGomes, Abel
dc.date.accessioned2020-01-15T11:27:10Z
dc.date.available2020-01-15T11:27:10Z
dc.date.issued2017
dc.description.abstractProtein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling ambiguity.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citation2017-Diaspt_PT
dc.identifier.doi10.1186/s12859-017-1913-4pt_PT
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10400.6/8304
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherBMCpt_PT
dc.relationSHAPE REPRESENTATION AND RECOGNITION METHODS IN MOLECULAR DOCKING
dc.relation.publisherversionhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1913-4pt_PT
dc.subjectProtein cavitypt_PT
dc.subjectProtein pocketpt_PT
dc.subjectGeometric detection of pocketspt_PT
dc.subjectGPU computingpt_PT
dc.titleGPU-Based De- tection of Protein Cavities using Gaussian Surfacespt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleSHAPE REPRESENTATION AND RECOGNITION METHODS IN MOLECULAR DOCKING
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/FARH/SFRH%2FBD%2F69829%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/UTAP-EXPL%2FQEQ-COM%2F0019%2F2014/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FEEA%2F50008%2F2013/PT
oaire.citation.endPage10pt_PT
oaire.citation.issue493pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleBMC Bioinformaticspt_PT
oaire.citation.volume18pt_PT
oaire.fundingStreamFARH
oaire.fundingStream3599-PPCDT
oaire.fundingStream5876
person.familyNameDias
person.familyNameMartins
person.familyNamePadrão Gomes
person.givenNameSérgio
person.givenNameAna Mafalda
person.givenNameAbel João
person.identifierJ-8234-2017
person.identifierH-9602-2014
person.identifier.ciencia-id0512-AF85-D322
person.identifier.ciencia-idFA1E-2B03-AB86
person.identifier.ciencia-idEC1D-4ACD-6A62
person.identifier.orcid0000-0002-9752-9386
person.identifier.orcid0000-0002-7832-4430
person.identifier.orcid0000-0002-5804-5717
person.identifier.scopus-author-id36668366300
person.identifier.scopus-author-id14054576600
person.identifier.scopus-author-id8325080300
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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