Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis.

@article{Opron2014FastAA,
  title={Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis.},
  author={Kristopher Opron and Kelin Xia and Guowei Wei},
  journal={The Journal of chemical physics},
  year={2014},
  volume={140 23},
  pages={
          234105
        }
}
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… 
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References

SHOWING 1-10 OF 56 REFERENCES
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.
  • Tirion
  • Chemistry
    Physical review letters
  • 1996
TLDR
It is shown that a single-parameter potential is sufficient to reproduce the slow dynamics of proteins obtained with vastly more complex empirical potentials, which inevitably leads to unstable modes which must be eliminated through elaborate methods, and which cast doubts on the validity of the analysis.
Protein flexibility predictions using graph theory
TLDR
This novel computational procedure is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side‐chains from analysis of a single, static three‐dimensional structure.
Structural flexibility in proteins: impact of the crystal environment
TLDR
An elastic network model is developed for the whole protein crystal in order to study the influence of crystal packing and lattice vibrations on the thermal fluctuations of the atom positions and the main findings are crystal packing modifies the atomic fluctuations considerably and thermal fluctuations are not the dominant contribution to crystallographic Debye-Waller factors.
A comparative study of motor-protein motions by using a simple elastic-network model
  • Wenjun Zheng, S. Doniach
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
A surprising dichotomy is found between kinesins and the other motor proteins (myosins and F1-ATPase) using a version of the simple elastic-network model of large-scale protein motions originally proposed by Tirion, which may suggest the presence of two different mechanisms for myosin and kinesin, despite their strong evolutionary ties and structural similarities.
Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability
A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartitio
Molecular mechanisms of chaperonin GroEL-GroES function.
The dynamics of the GroEL-GroES complex is investigated with a coarse-grained model. This model is one in which single-residue points are connected to other such points, which are nearby, by
...
...