Computational Chemistry and Molecular Modeling
Wiley InterScience Backfile Collection 1832-2000
Chemistry and Pharmacology
We address the problem of marking points on a grid lattice of arbitrary size and spacing as either accessible or inaccessible to a solvent-sized spherical probe. It is shown that an analytical description of the solvent-accessible volume suitable for rapidly testing a large number of lattice points can be constructed from relatively simple geometric elements. By first constructing these basic analytical elements and storing them in suitable data structures, any number of subsequent lattice markings can be carried out. This approach leads to increased computational efficiency whenever a multiple calculation using different lattice sizes and scales is necessary on the same molecular geometry. We also present an algorithm for determining the analytical volume elements. Some aspects of this algorithm, particularly the method for finding all sterically allowed probe positions in which the probe simultaneously contacts three atoms, may also be useful for improving the speed and reliability of analytical surface area calculations. An object-oriented implementation of these algorithms written in C + + is freely available via Internet. © 1995 by John Wiley & Sons, Inc.
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