ANALYTICALLY DEFINED SURFACES TO ANALYZE MOLECULAR INTERACTION PROPERTIES

Molecular surfaces are widely used for characterizing molecules and di splaying and quantifying their interaction properties. Here we conside r molecular surfaces defined as isocontours of a function (a sum of ex ponential functions centered on each atom) that approximately represen ts electron density. The smoothness is advantageous for surface mappin g of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defin ed surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, o bviating the necessity to compute values of the property on an array o f surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purpo ses. Applications to studies of protein-protein interactions are descr ibed. (C) 1996 by Elsevier Science, Inc.