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Fast and accurate computation schemes for evaluating vibrational entropy of proteins
Author(s) -
Xu Beisi,
Shen Hujun,
Zhu Xiao,
Li Guohui
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21900
Subject(s) - computation , statistical physics , entropy (arrow of time) , computer science , algorithm , mathematics , physics , thermodynamics
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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011