Generalized flexibility-rigidity index

Duc Duy Nguyen, Kelin Xia, Guo Wei Wei

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


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.

Original languageEnglish
Article number234106
JournalJournal of Chemical Physics
Issue number23
StatePublished - Jun 21 2016

Bibliographical note

Publisher Copyright:
© 2016 Author(s).

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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