Journal
PROTEIN ENGINEERING
Volume 15, Issue 12, Pages 959-965Publisher
OXFORD UNIV PRESS
DOI: 10.1093/protein/15.12.959
Keywords
binary operations; hydrophobic effect; implicit solvent; molecular graphics; molecular simulations; molecular surface; water
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A fast algorithm for computing the solvent-accessible molecular surface area (SAS) using Boolean masks [Le Grand,S.M. and Merz,K.M.J. (1993). J. Comput. Chem., 14, 349-352) has been modified to estimate the solvent-excluded molecular surface area (SES), including contact, toroidal and re-entrant surface components. Numerical estimates of arc lengths of intersecting atomic SAS are used to estimate the toroidal surface and intersections between those arcs are used to estimate the re-entrant surface area. The new method is compared with an exact analytical method. Boolean molecular surface areas are continuous and pairwise differentiable and should be useful for molecular dynamics simulations, especially as the basis for an implicit solvent model.
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