New Structure Deformation Algorithm for Monte Carlo Simulation of Protein Folding

Toshiyuki MEGURO and Ichiro YAMATO*

Department of Biological Science and Technology, Science University of Tokyo
2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan

(Received: October 30, 2001; Accepted for publication: January 9, 2002; Published on Web: March 22, 2002)

We developed a new conformational deformation algorithm (parallel translation method) for the Monte Carlo (MC)method to study the folding of biological macromolecules.
By comparing the structures obtained using the parallel translation algorithm with those obtained using the conventional algorithm (dihedral rotation method), we found that the structure forming tendency by MC simulation using the parallel translation algorithm was different from that using the dihedral rotation algorithm even under the same force field parameters. Dihedral rotation algorithm was effective for C-peptide(single a-helix structure, 13-mer) folding simulation. On the other hand, the parallel translation algorithm was more effective for 28-mer( b b a structure) folding simulation.
With better force field parameters, the parallel translation method will become useful for practical folding simulation of biomacromolecules.

Keywords: Monte Carlo simulation, Protein folding, Parallel translation method

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