A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

By J. A. Grant, M. A. Gallardo, B. T. Pickup. 1996

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Citations in the corpus

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles (2011, methodology): “The molecular shape quadrupoles in the principal-axes frame [9,13] are given as the following:”
PubChem3D: Similar conformers (2011, background): “One of these is the shape Tanimoto (ST) for shape similarity [10-12, 16, 17 where V AA and V BB are the respective self-overlap volume and V AB is the overlap volume of conformers A and B. where, for each of the six independent fictitious feature atom types, V AA and V BB are the respective…”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, unknown): “A variety of ligandbased shape comparison methods have been developed for aligning pairs of molecules on the basis of volume overlap [37,38]; a convenient modern implementation of this approach is the ROCS software (OpenEye Scientific Software, Santa Fe, NM) [39,40].”
PubChem3D: Diversity of shape (2011, methodology): “One successful virtual screening approach is to compare the 3-D shape similarity of chemical structures using atomcentered Gaussian functions [9-11], e.”
PubChem3D: Conformer generation (2011, background): “where VAA and VBB are the self-overlap volume of A and B, respectively, and VAB is the overlap volume between A and B [24-26].”
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis (2012, methodology): “Our previous study [10] attempted to address this question in part, by investigating the distributions of the Rapid Overlay of Chemical Structures (ROCS) [13-21]based 3-D similarity scores used in PubChem3D [8,10,11] between 270 billion unique compound pairs arising from 734,485 biologically tested ”
PubChem3D: a new resource for scientists (2011, background): “…indexes for “ Volume3D ” , “ XStericQuadrupole3D ” , “ YStericQuadrupole3D ” , and “ ZStericQuadrupole3D ” correspond, respectively, to the analytic volume and the three steric quadrupole moments [9,12,42] for only the first conformer in the diverse conformer list ( i.e. , the default conformer).”