title: CABS-flex predictions of protein flexibility compared with NMR ensembles.
abstract: BACKGROUND
  Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.
  
  
  RESULTS
  Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes.
  
  
  METHODS
  The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex.
  
  
  BACKGROUND
  sekmi@chem.uw.edu.pl
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Jamroz
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
mesh_terms: D019295:Computational Biology; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
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