6533b828fe1ef96bd1288c51

RESEARCH PRODUCT

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

Iñaki TuñónEstanislao SillaJuan-luis Pascual-ahuir

subject

Surface (mathematics)ComputationVolume (computing)Van der Waals surfaceGeneral ChemistryFunction (mathematics)Accessible surface areaSet (abstract data type)Computational Mathematicssymbols.namesakesymbolsSPHERESAlgorithmMathematics

description

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.

yearjournalcountryeditionlanguage
1994-10-01Journal of Computational Chemistry
https://doi.org/10.1002/jcc.540151009