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

✍ Scribed by Weiser, J�rg; Shenkin, Peter S.; Still, W. Clark

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
337 KB
Volume
20
Category
Article
ISSN
0192-8651

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✦ Synopsis

We explored the use of several breadth-first and depth-first algorithms for the computation of Gaussian atomic and molecular surface areas. Ž . 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 Ž . 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 ˚2 average absolute atomic error of 1.16 A with respect to the hard-sphere atomic SASA results in 7 s of CPU time on an R10000r194 MHz processor. Speed and accuracy were both optimized for SASA by the use of neighbor-list reduction Ž . Ž . 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.

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