Premium
Optimization of Gaussian surface calculations and extension to solvent‐accessible surface areas
Author(s) -
Weiser Jörg,
Shenkin Peter S.,
Still W. Clark
Publication year - 1999
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/(sici)1096-987x(199905)20:7<688::aid-jcc4>3.0.co;2-f
Subject(s) - sasa , atom (system on chip) , accessible surface area , computation , surface (topology) , van der waals force , gaussian , algorithm , van der waals radius , chemistry , mathematics , computational chemistry , computer science , molecule , physics , quantum mechanics , geometry , paleontology , biology , embedded system
We explored the use of several breadth‐first and depth‐first algorithms for the computation of Gaussian atomic and molecular surface areas. Our results for whole‐molecule van der Waals surface areas (vdWSAs) were 10 times more accurate in relative error, relative to actual hard‐sphere areas, than those reported by earlier workers. We were also able to extend the method to the computation of solvent‐accessible surface areas (SASAs). This was made possible by an appropriate combination of algorithms, parameters, and preprocessing steps. For united‐atom 3app, a 2366‐atom protein, we obtained an average absolute atomic error of 1.16 Å 2 with respect to the hard‐sphere atomic SASA results in 7 s of CPU time on an R10000/194 MHz processor. Speed and accuracy were both optimized for SASA by the use of neighbor‐list reduction (NLR), buried‐atom elimination (BAE), and a depth‐first search of the tree of atomic intersections. Accuracy was further optimized by the application of atom type specific parameters to the raw Gaussian results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 688–703, 1999