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CONFLEX: Conformational Behaviors of Polypeptides as Predicted by a Conformational Space Search

H. Goto, T. Takahashi, Y. Takata, K. Ohta and U. Nagashima
Toyohashi University of Technology, JP

Keywords: Protein Folding, Conformational Space Search, Molecular Mechanics

Abstract:
The elucidation of the stable conformations and the folding process of proteins is one of the most fundamental and challenging goals in life science. While some of the most common secondary structures (e.g., a few types of helix, beta-sheet) have been well-known, the million numbers of the chemically important conformers and picoseconds order of their conformational interconversions via the transition states on the potential energy surface will be required for the study of the microseconds order of folding process toward the tertiary structure formations. CONFLEX has been known as one of the most efficient reliable conformational space search programs. Recently, we have applied a high-performance computing technique into this program, and suggested that the performance of the parallelized CONFLEX enables to explore the lower-energy region of the conformational space of small peptides within an available elapsed time using PC cluster. In this conference, we will also report our method for predicting some folding processes of small polypeptides by the precise conformational analyses based on the ten thousands number of conformers found by “Parallel CONFLEX”. Acknowledgement: Financial support by Japan Ministry of Education, Culture, Sports, Science and Technology (Grant-in-Aid for the Development of Innovative Technology: No.12413) is highly acknowledged.

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