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An Improved Free Energy Formulation and Implementation for Kinetostatic Protein Folding Simulation

[+] Author Affiliations
Pouya Tavousi, Morad Behandish, Kazem Kazerounian, Horea T. Ilieş

University of Connecticut, Storrs, CT

Paper No. DETC2013-12671, pp. V06AT07A006; 13 pages
doi:10.1115/DETC2013-12671
From:
  • 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
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-5593-5
  • Copyright © 2013 by ASME

abstract

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.

Copyright © 2013 by ASME
Topics: Simulation , Proteins

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