Protein structure prediction remains one of the significant challenges in computational biology. We have previously shown that our kinetostatic compliance method can overcome some of the key difficulties faced by other de novo structural prediction methods, such as the very small time steps required by the molecular dynamics approaches, or the very large number of samples required by the sampling based techniques. In this paper we extend the previous free energy formulation by adding the solvent effects, which contribute predominantly to the folding phenomena. We show that the addition of the solvation effects, which complement the existing Coulombic and van der Waals interactions, lead to a physically effective energy function. Furthermore, we achieve significant computational speed-up by employing efficient algorithms and data structures that effectively reduce the time complexity from O(n2) to O(n), n being the number of atoms. Our simulations are consistent with the general behavior observed in protein folding, and show that the hydrophobic atoms tend to pack inside the core of the molecule in an aqueous solvent, while a vacuum environment produces no such effect.
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ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
August 4–7, 2013
Portland, Oregon, USA
Conference Sponsors:
- Design Engineering Division
- Computers and Information in Engineering Division
ISBN:
978-0-7918-5593-5
PROCEEDINGS PAPER
An Improved Free Energy Formulation and Implementation for Kinetostatic Protein Folding Simulation Available to Purchase
Pouya Tavousi,
Pouya Tavousi
University of Connecticut, Storrs, CT
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Morad Behandish,
Morad Behandish
University of Connecticut, Storrs, CT
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Kazem Kazerounian,
Kazem Kazerounian
University of Connecticut, Storrs, CT
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Horea T. Ilieş
Horea T. Ilieş
University of Connecticut, Storrs, CT
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Pouya Tavousi
University of Connecticut, Storrs, CT
Morad Behandish
University of Connecticut, Storrs, CT
Kazem Kazerounian
University of Connecticut, Storrs, CT
Horea T. Ilieş
University of Connecticut, Storrs, CT
Paper No:
DETC2013-12671, V06AT07A006; 13 pages
Published Online:
February 12, 2014
Citation
Tavousi, P, Behandish, M, Kazerounian, K, & Ilieş, HT. "An Improved Free Energy Formulation and Implementation for Kinetostatic Protein Folding Simulation." Proceedings of the ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. Volume 6A: 37th Mechanisms and Robotics Conference. Portland, Oregon, USA. August 4–7, 2013. V06AT07A006. ASME. https://doi.org/10.1115/DETC2013-12671
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