Protein Motion Simulation Algorithm for Dihedral Angle Rotation Implementing Variable Speed

Abstract

Most methodologies used for protein motion simulation either require a high computational cost, or the produced results do not fulfill kinematics requirements. For instance, molecular dynamics, which obtains the most accurate results, is hardly used to simulate proteins’ big conformational changes because of its huge computational requirements. Faster simulation methods, like interpolation procedures, do not produce realistic intermediate positions, mostly because of impossible kinematics between consecutive positions of the motion. In this paper, a new procedure is presented which simulates protein motion with affordable computational requirements. The procedure uses dihedral angle increments to produce the protein motion avoiding any energy minimization process. The kinematic model used for the protein structure is based on the ball and rods approach and is further refined by a normalization method to reduce experimental methods induced errors.

Keywords:

• Folding
• Kinematics
• Molecular mechanism
• Proteins
• Serial robot

Notes

^#Communicated by G. K. Ananthasuresh.

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