Conformation Analysis of Enkephalin Using Hamiltonian Algorithm
- Effect of Mixing Coefficient in HA -

Kyouhei TSUCHIYAa, Hiroyuki TERAMAEa*, Toshio WATANABEb, c, Takayoshi ISHIMOTOb, c and Umpei NAGASHIMAb, c

aDepartment of Chemistry, Faculty of Science, Josai University
1-1 Keyakidai, Sakado, Saitama 350-0295, Japan.
bResearch Institute for Computational Science, National Institute of Advanced Industrial Science and Technology
1-1-1Umezono, Tsukuba, Ibaraki 305-8568, Japan,
cCore Research for Revolutional Science and Technology, Japan Science and Technology Agency
4-1-8 Honmchi, Kawaguchi, Saitama 332-0012, Japan.

(Received: April 26, 2007; Accepted for publication: October 25, 2007; Published on Web: December 3, 2007)

In order to execute molecular dynamics (MD) simulation for the holding process and native structure of proteins efficiently, Hamiltonian algorithm (HA) was equipped to an MD program: PEACH. The difference between the conventional method and HA is evaluated using Leu-Enkephalin and Met-Enkephalin. HA was efficient for sampling a wide area of geometrical space because many low energy conformations were observed along trajectories of HA.

Keywords: Molecular dynamics, Hamiltonian algorithm, Native structure of protein, Holding process of protein, Enkephalin


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