Memoirs of the Faculty of Science, Shimane University

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Memoirs of the Faculty of Science, Shimane University 24
1990-12-25 発行

任意の分岐した側鎖をもつタンパク質のコンフォーメーショナル・エネルギーの2次微分の並列アルゴリズム

A Parallel Algorithm to Calculate Second Derivatives of Conformational Energy in Proteins with Any Branched Sidechains
Hara, Heihachiro
Kayano, Takashi
Kanahiro, Kazuhiko
Go, Nobuhiro
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Description
A protein molecule can be regarded as a set of rigid units and rotatable bonds. We present here a parallel algorithm of calculations for second derivative matrix with respect to dihedral angles around bonds for proteins with any branched side chains. The basic idea of the algorithm for processor array type computers is the introduction of the nearest outside units and related quantities. A method of initial setting and transfer of bond data is also presented in simple mathematical expressions which are easily coded in the computer program.