Predicting Real-Valued Protein Residue Fluctuation Using FlexPred

Methods Mol Biol. 2017;1484:175-186. doi: 10.1007/978-1-4939-6406-2_13.

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/ .

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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • Crystallography, X-Ray
  • Databases, Protein
  • Magnetic Resonance Spectroscopy
  • Molecular Dynamics Simulation
  • Protein Conformation*
  • Proteins / chemistry
  • Proteins / genetics*
  • Software*

Substances

  • Proteins