A Comparison of Kinetostatic and Multibody Dynamics Models for Simulating Protein Structures

This paper presents an initial comparison of two approaches to energy minimization of protein molecules, namely the Molecular Dynamic Simulation and the Kineto-Static Compliance Method. Both methods are well established and are promising contenders to the seemingly insurmountable task of global optimization in the protein molecules potential energy terrain. The Molecular Dynamic Simulation takes the form of Constrained Multibody Dynamics of interconnected rigid bodies, as implemented at the Virtual Reality Application Center from Iowa State University. The Kineto-Static Compliance Method is implemented in the Protofold Computer package developed in the Mechanical Engineering Department at the University of Connecticut. The simulation results of both methods are compared through the trajectory of potential energy, the Root Mean Square Deviation (RMSD) of the alpha carbons, as well as based on visual observations. The preliminary results indicate that both techniques are very effective in converging the protein structure to a state with significantly less potential energy. At present, the converged solutions for the two methods are, however, different from each other and are very likely different from the global minimum potential energy state.Copyright © 2007 by ASME