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

Hiroshi Wako, Nobuhiro Gō

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)625-635
Number of pages11
JournalJournal of Computational Chemistry
Volume8
Issue number5
DOIs
Publication statusPublished - 1987
Externally publishedYes

Fingerprint

Supercomputers
Supercomputer
Energy Function
Proteins
Protein
Dihedral angle
Coulomb interactions
Interaction
Hessian matrix
Pipelines
Long-range Interactions
Electrostatics
Pairwise
Benchmark
Energy

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer. / Wako, Hiroshi; Gō, Nobuhiro.

In: Journal of Computational Chemistry, Vol. 8, No. 5, 1987, p. 625-635.

Research output: Contribution to journalArticle

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