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 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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July 2005
Technical Papers
Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction
Kazem Kazerounian,
Kazem Kazerounian
Professor
ASME Fellow
Mechanical Engineering Department,
University of Connecticut
, Storrs, CT 06269-3139
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Khalid Latif,
Khalid Latif
Graduate Student
Mechanical Engineering Department,
University of Connecticut
, Storrs, CT 06269-3139
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Carlos Alvarado
Carlos Alvarado
Assistant Professor
Polytechnic University of Puerto Rico
, Hato Rey, PR 00918
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Kazem Kazerounian
Professor
ASME Fellow
Mechanical Engineering Department,
University of Connecticut
, Storrs, CT 06269-3139
Khalid Latif
Graduate Student
Mechanical Engineering Department,
University of Connecticut
, Storrs, CT 06269-3139
Carlos Alvarado
Assistant Professor
Polytechnic University of Puerto Rico
, Hato Rey, PR 00918J. Mech. Des. Jul 2005, 127(4): 712-717 (6 pages)
Published Online: August 5, 2004
Article history
Received:
February 16, 2004
Revised:
August 5, 2004
Citation
Kazerounian, K., Latif, K., and Alvarado, C. (August 5, 2004). "Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction." ASME. J. Mech. Des. July 2005; 127(4): 712–717. https://doi.org/10.1115/1.1867502
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