Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/82116
Title: Stochastic model for protein flexibility analysis
Authors: Xia, Kelin
Wei, Guo-Wei
Keywords: Science
Physics
Issue Date: 2013
Source: Xia, K., & Wei, G.-W. (2013). Stochastic model for protein flexibility analysis. Physical Review E, 88, 062709-.
Series/Report no.: Physical Review E
Abstract: Protein flexibility is an intrinsic property and plays a fundamental role in protein functions. Computational analysis of protein flexibility is crucial to protein function prediction, macromolecular flexible docking, and rational drug design. Most current approaches for protein flexibility analysis are based on Hamiltonian mechanics. We introduce a stochastic model to study protein flexibility. The essential idea is to analyze the free induction decay of a perturbed protein structural probability, which satisfies the master equation. The transition probability matrix is constructed by using probability density estimators including monotonically decreasing radial basis functions. We show that the proposed stochastic model gives rise to some of the best predictions of Debye-Waller factors or B factors for three sets of protein data introduced in the literature.
URI: https://hdl.handle.net/10356/82116
http://hdl.handle.net/10220/41117
ISSN: 1539-3755
DOI: 10.1103/PhysRevE.88.062709
Rights: © 2013 American Physical Society. This paper was published in Physical Review E and is made available as an electronic reprint (preprint) with permission of American Physical Society. The published version is available at: [http://dx.doi.org/10.1103/PhysRevE.88.062709]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SPMS Journal Articles

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