Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of
Skip Nav Destination
Article navigation
21 June 2014
Research Article|
June 17 2014
Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis
Kristopher Opron;
Kristopher Opron
1Department of Biochemistry and Molecular Biology,
Michigan State University
, Michigan 48824, USA
Search for other works by this author on:
Kelin Xia;
Kelin Xia
2Department of Mathematics,
Michigan State University
, Michigan 48824, USA
Search for other works by this author on:
Guo-Wei Wei
Guo-Wei Wei
a)
1Department of Biochemistry and Molecular Biology,
Michigan State University
, Michigan 48824, USA
2Department of Mathematics,
Michigan State University
, Michigan 48824, USA
3Department of Electrical and Computer Engineering,
Michigan State University
, Michigan 48824, USA
Search for other works by this author on:
a)
Author to whom correspondence should be addressed. Electronic mail: [email protected]
J. Chem. Phys. 140, 234105 (2014)
Article history
Received:
December 31 2013
Accepted:
May 24 2014
Citation
Kristopher Opron, Kelin Xia, Guo-Wei Wei; Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis. J. Chem. Phys. 21 June 2014; 140 (23): 234105. https://doi.org/10.1063/1.4882258
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
Freezing point depression of salt aqueous solutions using the Madrid-2019 model
Cintia P. Lamas, Carlos Vega, et al.
Related Content
Multiscale weighted colored graphs for protein flexibility and rigidity analysis
J. Chem. Phys. (February 2018)
Generalized flexibility-rigidity index
J. Chem. Phys. (June 2016)
Blind prediction of protein B-factor and flexibility
J. Chem. Phys. (October 2018)
Communication: Capturing protein multiscale thermal fluctuations
J. Chem. Phys. (June 2015)
Multiscale multiphysics and multidomain models—Flexibility and rigidity
J. Chem. Phys. (November 2013)