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Title: Generalized flexibility-rigidity index
Authors: Nguyen, Duc Duy
Xia, Kelin
Wei, Guo-Wei
Keywords: Anisotropy
Issue Date: 2016
Source: Nguyen, D. D., Xia, K., & Wei, G.-W. (2016). Generalized flexibility-rigidity index. The Journal of Chemical Physics, 144(23), 234106-.
Series/Report no.: The Journal of Chemical Physics
Abstract: Flexibility-rigidity index (FRI) has been developed as a robust, accurate, and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility index. In this work, we introduce alternative rigidity and flexibility formulations. The structure of the classic Gaussian surface is utilized to construct a new type of rigidity index, which leads to a new class of rigidity densities with the classic Gaussian surface as a special case. Additionally, we introduce a new type of flexibility index based on the domain indicator property of normalized rigidity density. These generalized FRI (gFRI) methods have been extensively validated by the B-factor predictions of 364 proteins. Significantly outperforming the classic Gaussian network model, gFRI is a new generation of methodologies for accurate, robust, and efficient analysis of protein flexibility and fluctuation. Finally, gFRI based molecular surface generation and flexibility visualization are demonstrated.
ISSN: 0021-9606
DOI: 10.1063/1.4953851
Schools: School of Physical and Mathematical Sciences 
Rights: © 2016 American Institute of Physics. This paper was published in The Journal of Chemical Physics and is made available as an electronic reprint (preprint) with permission of American Institute of Physics. The published version is available at: []. 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
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