Predicting Real-Valued Protein Residue Fluctuation Using FlexPred

  • Lenna Peterson
  • Michal Jamroz
  • Andrzej Kolinski
  • Daisuke Kihara
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1484)

Abstract

The conventional view of a protein structure as static provides only a limited picture. There is increasing evidence that protein dynamics are often vital to protein function including interaction with partners such as other proteins, nucleic acids, and small molecules. Considering flexibility is also important in applications such as computational protein docking and protein design. While residue flexibility is partially indicated by experimental measures such as the B-factor from X-ray crystallography and ensemble fluctuation from nuclear magnetic resonance (NMR) spectroscopy as well as computational molecular dynamics (MD) simulation, these techniques are resource-intensive. In this chapter, we describe the web server and stand-alone version of FlexPred, which rapidly predicts absolute per-residue fluctuation from a three-dimensional protein structure. On a set of 592 nonredundant structures, comparing the fluctuations predicted by FlexPred to the observed fluctuations in MD simulations showed an average correlation coefficient of 0.669 and an average root mean square error of 1.07 Å. FlexPred is available at http://kiharalab.org/flexPred/.

Key words

Bioinformatics Computational biology Support vector machine Support vector regression Protein residue fluctuation Protein flexibility Protein conformational flexibility Protein structure Protein design Molecular dynamics 

Notes

Acknowledgements

This work was partly supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM097528) and the National Science Foundation (IIS1319551, DBI1262189, IOS1127027).

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Lenna Peterson
    • 1
  • Michal Jamroz
    • 2
  • Andrzej Kolinski
    • 2
  • Daisuke Kihara
    • 1
    • 3
  1. 1.Department of Biological Sciences, College of SciencePurdue UniversityWest LafayetteUSA
  2. 2.Laboratory of Theory of Biopolymers, Faculty of ChemistryUniversity of WarsawWarszawaPoland
  3. 3.Department of Computer Science, College of SciencePurdue UniversityWest LafayetteUSA

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