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AuthorYilmazer, Nusret Duygudc.contributor.author
Date of accession2020-11-04T12:49:53Zdc.date.accessioned
Available in OPARU since2020-11-04T12:49:53Zdc.date.available
Year of creation2015dc.date.created
Date of first publication2020-11-04dc.date.issued
AbstractComputing accurate protein-ligand interaction energies is essential for virtual drug design. For this purpose, in this work, the opportunities of applying fast, enhanced SQM methods are explored. The PDBbind set is used as the experimental reference for protein and ligand structures and binding affinities. As a part of this work, an algorithm is developed to prepare the structures for the computations. For the calculations, Gilson’s minima mining approach is followed, which reduces the problem of obtaining binding energies into computing optimized energies and vibrational frequencies for a large number of binding modes. Protein-ligand interaction energies are computed by various computational methods: i.e. semi empirical quantum mechanical (SQM) methods, Molecular Mechanical (MM) methods, Density functional theory (DFT) methods and Wave function theory (WFT) methods. The accuracy of the results are compared with each other and experimental binding energies. In total, three benchmarking studies are conducted. In all of them, PM6-DH+ performs as almost as accurate as DFT and WFT methods for realistic model systems, while being fast enough to be used for real protein-ligand systems within the minima mining approach.dc.description.abstract
Languageendc.language.iso
PublisherUniversität Ulmdc.publisher
Earlier versionhttp://dx.doi.org/10.18725/OPARU-3353dc.relation.isversionof
LicenseStandarddc.rights
Link to license texthttps://oparu.uni-ulm.de/xmlui/license_v3dc.rights.uri
KeywordBenchmarking methodsdc.subject
KeywordSemi-empirical quantum mechanical methodsdc.subject
KeywordVirtual drug designdc.subject
Dewey Decimal GroupDDC 610 / Medicine & healthdc.subject.ddc
MeSHComputational biologydc.subject.mesh
MeSHDrug designdc.subject.mesh
MeSHMolecular biology; Methodsdc.subject.mesh
TitleComputational screening of energy- and bio-materialsdc.title
Resource typeDissertationdc.type
Date of acceptance2015-11-24dcterms.dateAccepted
RefereeKorth, Martindc.contributor.referee
RefereeTaubmann, Gerharddc.contributor.referee
DOIhttp://dx.doi.org/10.18725/OPARU-33638dc.identifier.doi
PPN1738057747dc.identifier.ppn
URNhttp://nbn-resolving.de/urn:nbn:de:bsz:289-oparu-33700-0dc.identifier.urn
GNDArzneimitteldesigndc.subject.gnd
GNDBiomaterialdc.subject.gnd
GNDComputational chemistrydc.subject.gnd
FacultyFakultät für Naturwissenschaftenuulm.affiliationGeneral
InstitutionInstitut für Theoretische Chemieuulm.affiliationSpecific
Grantor of degreeFakultät für Naturwissenschaftenuulm.thesisGrantor
DCMI TypeTextuulm.typeDCMI
CategoryPublikationenuulm.category
Bibliographyuulmuulm.bibliographie


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