Molecular Dynamics Simulation of Biological Molecules (2) Practice

Yuto KOMEIJIa, b, c*, Sumie TAJIMAd, e, Makoto HARAGUCHId, Nobuyuki TAKAHASHIf, Masami UEBAYASIc and Umpei NAGASHIMAa

aNational Institute for Advanced Interdisciplinary Research
1-1-4 Higashi, Tsukuba 305-8562, Japan
bElectrotechnical Laboratory
1-1-4 Umezono, Tsukuba 305-8568, Japan
cNational Institute of Bioscience and Human-Technology
1-1-3 Higashi, Tsukuba 305-8566, Japan
dBestsystems, Inc.
2-1-6 Sengen, Tsukuba 305-0047, Japan
eOchanomizu University
2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
fHokkaido University of Education
1-2 Yawata, Hakodate, Hokkaido, 040-8567

(Received: February 8, 2000; Accepted for publication: March 14, 2000; Published on Web: July 13, 2000)

Molecular dynamics simulation has been extensively applied to analyses of structure, dynamics, and the function of biological molecules. In this review, the practical procedures of molecular dynamics simulations of a protein and DNA by using the software PEACH (Program for Energetic Analysis of bioCHemical molecules) are described.

Keywords: Program for Energetic Analysis of bioCHemical molecules (PEACH), Molecular Dynamics (MD), Protein, DNA

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