ProtoFold: Part II — A Successive Kineto-Static Compliance Method for Protein Conformation Prediction

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 inter-atomic 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 zero. 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.