Journal
BIOINFORMATICS
Volume 30, Issue 15, Pages 2150-2154Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu184
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Funding
- EU European Regional Development Fund operated within the Innovative Economy Operational Program
- Polish National Science Centre [NN301071140]
- Polish Ministry of Science and Higher Education [IP2011 024371]
- Foundation for Polish Science TEAM project [TEAM/2011-7/6]
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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 protein regions that undergo conformational changes as well as the extent of such changes.
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