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. 1999 May;20(7):688-703.
doi: 10.1002/(SICI)1096-987X(199905)20:7<688::AID-JCC4>3.0.CO;2-F.

Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas

Jörg Weiser  1 , Peter S Shenkin  1 , W Clark Still  1
Affiliations

Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas

Jörg Weiser et al. J Comput Chem. 1999 May.

Abstract

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 Å2 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.

Keywords: Gaussian shape; breadth-first algorithm; buried atom elimination (BAE); depth-first algorithm; neighbor-list reduction (NLR); solvent-accessible surface area (SASA); van der Waals surface areas (vdWSA).

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