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GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
Author(s) -
PascualAhuir Juan Luis,
Silla Estanislao
Publication year - 1990
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540110907
Subject(s) - spheres , surface (topology) , set (abstract data type) , van der waals force , molecule , group (periodic table) , computer science , physics , mathematics , geometry , quantum mechanics , astronomy , programming language
The algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.