alexa Derivatives of molecular surface area and volume: simple and exact analytical formulas.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Computer Science & Systems Biology

Author(s): Klenin KV, Tristram F, Strunk T, Wenzel W

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Abstract The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library. Copyright © 2011 Wiley Periodicals, Inc. This article was published in J Comput Chem and referenced in Journal of Computer Science & Systems Biology

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