Protein simulation using fast volume preservation

Authors:
Min Hong;David Osguthorpe;Min-Hyung Choi
Affiliations:
Division of Computer Science and Engineering, Soonchunhyang University, Chungcheongnam-do, Korea;Pharmacology, University of Colorado at Denver and Health Sciences Center, Denver, CO;Department of Computer Science and Engineering, University of Colorado at Denver and Health Sciences Center, Denver, CO
Venue:
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part I
Year:
2006

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Abstract

Since empirical force fields computation requires a heavy computational cost, the simulation of complex protein structures is a time consuming process for predicting their configuration. To achieve fast but plausible global deformations of protein, we present an efficient and robust global shape based protein dynamics model using an implicit volume preservation method. A triangulated surface of the protein is generated using a marching cube algorithm in pre-processing time. The normal mode analysis based on motion data is used as a reference deformation of protein to estimate the necessary forces for protein movements. Our protein simulator provides a nice test-bed for initial screening of behavioral analysis to simulate various types of protein complexes.