Localization and quantitative evaluation of potent local binding sites on the accessible Lennard–jones surface

Alexander A. Cohen*, Shimon E. Shatzmiller

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

This article presents a new method for topological analysis of molecular surfaces. Explicit representation of the van der Waals interaction according to the Lennard‐Jones potential enabled determination of the function of the maximum radius of a hypothetical atomic probe in any location, r, inside the host's domain. The size of the spatial gradient of the maximal probe's volume (named the ξ value) at that location was found to be a good descriptor of the local shape of the host. Consequently, mapping of the host domain according to the ξ value could be used as a quantitative tool for localization of potent local binding sites. The proposed method is illustrated by mapping an organic host (calix[4]arene) as well as an enzyme (HIV‐aspartic protease). Analysis of the calix[4]arene derivative revealed that the proposed method reproduces immediately the known binding site of conic calix[4]arenes. The second test case demonstrated how the catalytic site of the enzyme could be disassembled into many local binding sites. Some of these sites, located according to the proposed method, were found to follow the shape of a known inhibitor of the enzyme in a complementary manner. © 1995 John Wiley & Sons, Inc.

Original languageEnglish
Pages (from-to)1459-1467
Number of pages9
JournalJournal of Computational Chemistry
Volume16
Issue number12
DOIs
StatePublished - Dec 1995

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