Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 32, Issue 15, Pages 3188-3193Publisher
WILEY-BLACKWELL
DOI: 10.1002/jcc.21900
Keywords
normal mode analysis; vibrational entropy; coarse-grained NMA
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Funding
- National High-tech Research and Development Program [2009AA01A137]
- National Natural Science Foundation of China [31070641/C050101]
- Chinese Academy Sciences
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Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. To evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse-grained NMA methods. This can be achieved by rescaling coarse-grained results with a specific factor that is derived on the basis of the linear correlation of protein vibrational entropy between standard NMA and coarse-grained NMA. Our coarse-grained NMA computation schemes can repeat correctly and efficiently the results of standard NMA for large proteins. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 3188-3193, 2011
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