GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent‐excluding surface

TLDR

Accurate molecular surface calculation is essential for modeling solute–solvent interactions, with common surfaces including van der Waals, Accessible, and Molecular surfaces, and GEPOL93 builds on earlier GEPOL versions with a new algorithm. This study redefines the molecular surface as the Solvent‑Excluding Surface. The algorithm constructs the Solvent‑Excluding Surface by filling inaccessible solvent spaces with new spheres, with parameters NDIV, OFAC, and RMIN controlling triangle density, sphere overlap, and minimum sphere size, and it estimates area and volume errors as a function of these parameters. The new algorithm, implemented in GEPOL93, is described and its changes make the program a distinct new tool rather than merely an updated version. © 1994 by John Wiley & Sons, Inc.

Abstract

Abstract To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent‐Excluding Surface. The new algorithm for computing the Solvent‐Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent‐Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.