Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces

Arun Malhotra, Robert K.‐Z Tan, Stephen C. Harvey

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron‐microscopy–based three‐dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.

Original languageEnglish (US)
Pages (from-to)190-199
Number of pages10
JournalJournal of Computational Chemistry
Volume15
Issue number2
DOIs
StatePublished - Feb 1994
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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