Journal
JOURNAL OF MECHANICAL DESIGN
Volume 127, Issue 4, Pages 712-717Publisher
ASME-AMER SOC MECHANICAL ENG
DOI: 10.1115/1.1867502
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This paper presents an efficient and novel computational protein prediction methodology called kineto-static compliance method. Successive kineto-static fold compliance is a methodology for predicting a protein molecule's motion under the effect of an interatomic force field without the need for molecular-dynamic simulation. Instead, the chain complies under the kineto-static effect of the force field in such a manner that each rotatable joint changes by an amount proportional to the effective torque on that joint. This process successively iterates until all of the joint torques have converged to a minimum. This configuration is equivalent to a stable, globally optimized potential energy state of the system or in other words, the final conformation of the protein. This methodology is implemented in a computer software package named PROTOFOLD. In this paper we have used PROTOFOLD to predict the final conformation of a small peptide chain segment, an alpha helix, and the Triponin protein chains from a denatured configuration. The results show that torques in each joint are minimized to values very close to zero, which demonstrates the method's effectiveness for protein conformation prediction.
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