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Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

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dc.abstract.enThe transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of great importance in biology and chemistry. UBDB2018 can be applied either as a source of aspherical atomic scattering factors in a standard X-ray experiment (dmin ’ 0.8 A ° ) instead of the independent atom model (IAM), and can therefore enhance the final crystal structure geometry and refinement parameters; or as a tool to reconstruct the molecular charge-density distribution and derive the electrostatic properties of chemical systems for which 3D structural data are available. The extended data bank has been extensively tested, with the focus being on the accuracy of the molecular electrostatic potential computed for important drug-like molecules, namely the HIV-1 protease inhibitors. The UBDB allows the reconstruction of the reference B3LYP/6-31G** potentials, with a root-mean-squared error of 0.015 e bohr1 computed for entire potential grids which span values from ca 200 e bohr1 to ca 0.1 e bohr1 and encompass both the inside and outside regions of a molecule. UBDB2018 is shown to be applicable to enhancing the physical meaning of the molecular electrostatic potential descriptors used to construct predictive quantitative structure–activity elationship/quantitative structure–property relationship (QSAR/QSPR) models for drug discovery studies. In addition, it is suggested that electron structure factors computed from UBDB2018 may significantly improve the interpretation of electrostatic potential maps measured experimentally by means of electron diffraction or single-particle cryo-EM methods.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorBojarowski, Sławomir
dc.contributor.authorGruza, Brabara
dc.contributor.authorDominiak, Paulina
dc.contributor.authorKumar, Prashant
dc.date.accessioned2024-01-25T00:11:10Z
dc.date.available2024-01-25T00:11:10Z
dc.date.issued2019
dc.description.financeNie dotyczy
dc.description.volumeA75
dc.identifier.doi10.1107/S2053273319000482
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/106863
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofActa Crystallographica Section A: Foundations and Advances
dc.relation.pages398-408
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enquantum crystallography
dc.subject.enpseudoatom data bank
dc.subject.enUBDB2018
dc.subject.enaspherical scattering factors
dc.subject.enelectrostatic potential
dc.subject.entransferable aspherical atom model (TAAM)
dc.subject.enstructure refinement
dc.subject.enX-ray diffraction
dc.subject.enelectron diffraction
dc.subject.enelectron crystallography
dc.titleExtension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies
dc.typeJournalArticle
dspace.entity.typePublication