Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods
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- 作者：Summer Kassema ; Marawan Ahmedb ; Salah El-Sheikha ; Khaled H. Barakatb ; c ; d ; kbarakat@ualberta.ca" class="auth_mail" title="E-mail the corresponding author
- 关键词：Entropy ; Normal mode analysis ; Quasi harmonics ; Binding affinity ; Mining minima ; Configurational entropy
- 刊名：Journal of Molecular Graphics and Modelling
- 出版年：2015
- 出版时间：November 2015
- 年：2015
- 卷：62
- 期：Complete
- 页码：105-117
- 全文大小：1094 K
文摘
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Entropy is a major component of the binding affinity in biomolecular interactions.
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Most methods relate entropy to the atomic fluctuations spanned during simulations.
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The pioneering methods reviewed are NMA, QH, MM, NN, while recent approaches include MIST and MIE.
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While recent methods seem to be more accurate, they still suffer from a convergence problem.
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The pioneering methods predict the upper bound of the entropy.