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

Hiroshi Wako, Nobuhiro Gō

研究成果: Article査読

44 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)625-635
ページ数11
ジャーナルJournal of Computational Chemistry
8
5
DOI
出版ステータスPublished - 1987
外部発表はい

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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