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Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer

✍ Scribed by Hiroshi Wako; Nobuhiro Gō

Publisher
John Wiley and Sons
Year
1987
Tongue
English
Weight
919 KB
Volume
8
Category
Article
ISSN
0192-8651

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✦ Synopsis

An improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long-range, nonbonded interactions are cut off and long-range electrostatic interactions are approximated by dipole-dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different sizes.

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