Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 19, Issue 3-4, Pages 325-+Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/S1093-3263(00)00079-6
Keywords
molecular shape; molecular surface; molecular recognition; shape complementarity; protein cavities; protein binding site; atomic density; fast Fourier transform
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Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules. (C) 2001 by EEsevier Science Inc.
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