Related ArticlesCABS-flex predictions of protein flexibility compared with NMR ensembles.
Bioinformatics. 2014 Apr 15;
Authors: Jamroz M, Kolinski A, Kmiecik S
Abstract
MOTIVATION: 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 of protein regions that undergo conformational changes and the extent of such changes.
AVAILABILITY: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex.
CONTACT: sekmi@chem.uw.edu.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID: 24735558 [PubMed - as supplied by publisher]
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Programs for alignment of protein NMR ensembles
If you need to align models in your NMR ensemble, you can use the following programs to do so. MolMol
- Official website
- Linux binaries from Patrick Finerty website
- BioXRay distribution
SuperPose server
Suppose
CABS-flex predictions of protein flexibility compared with NMR ensembles.
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