J Chem Inf Model - COSMOsim3D: 3D-similarity and alignment based on COSMO polarization charge densities.

Tópicos

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Resumo

COSMO s-surfaces resulting from quantum chemical calculations of molecules in a simulated conductor, and their histograms, the so-called s-profiles, are widely proven to provide a very suitable and almost complete basis for the description of molecular interactions in condensed systems. The COSMOsim method therefore introduced a global measure of molecular similarity on the basis of similarity of s-profiles, but it had the disadvantage of neglecting the 3D distribution of molecular polarities, which is crucially determining all ligand-receptor binding. This disadvantage is now overcome by COSMOsim3D, which is a logical and physically sound extension of the COSMOsim method, which uses local s-profiles on a spatial grid. This new method is used to measure intermolecular similarities on the basis of the 3D representation of the surface polarization charge densities s of the target and the probe molecule. The probe molecule is translated and rotated in space in order to maximize the sum of local s-profile similarities between target and probe. This sum, the COSMOsim3D similarity, is a powerful descriptor of ligand similarity and allows for a good discrimination between bioisosters and random pairs. Validation experiments using about 600 pharmacological activity classes in the MDDR database are given. Furthermore, COSMOsim3D represents a unique and very robust method for a field-based ligand-ligand alignment.

Resumo Limpo

cosmo ssurfac result quantum chemic calcul molecul simul conductor histogram socal sprofil wide proven provid suitabl almost complet basi descript molecular interact condens system cosmosim method therefor introduc global measur molecular similar basi similar sprofil disadvantag neglect d distribut molecular polar crucial determin ligandreceptor bind disadvantag now overcom cosmosimd logic physic sound extens cosmosim method use local sprofil spatial grid new method use measur intermolecular similar basi d represent surfac polar charg densiti s target probe molecul probe molecul translat rotat space order maxim sum local sprofil similar target probe sum cosmosimd similar power descriptor ligand similar allow good discrimin bioisost random pair valid experi use pharmacolog activ class mddr databas given furthermor cosmosimd repres uniqu robust method fieldbas ligandligand align

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