UTILIZATION OF SHAPE DATA IN MOLECULAR MECHANICS USING A POTENTIAL BASED ON SPHERICAL HARMONIC SURFACES

This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shap e data are provided by techniques such as electron-microscopy-based th ree-dimensional image reconstruction for large macromolecular assembli es. Such data can provide important constraints for molecular mechanic s. We represent topographical data by spherical harmonic surfaces, fir st used by Max and Getzoff(21) for displaying molecular surfaces. A si mple harmonic potential is used to constrain atoms within these spheri cal harmonic surfaces. This potential was implemented in the yammp mol ecular mechanics package.(27) Implementation details and results of se veral test cases are discussed here. (C) 1994 by John Wiley and Sons, Inc.