Comparative estimation of vibrational entropy changes in proteins through normal modes analysis

Journal of Molecular Graphics & Modelling
Benjamin J Carrington, Ricardo L Mancera

Abstract

We compare the vibrational entropy changes of proteins calculated using a full and a number of approximate normal modes analysis methods. The vibrational entropy differences for three conformational changes and three protein binding interactions were computed. In general, the approximate methods yield good estimates of the vibrational entropy change in a fraction of the time required by full normal modes analysis. The absolute entropies are either overestimated or greatly underestimated, but the difference is sufficiently accurate for some methods. This indicates that some of the approximate methods can give reasonable estimates of the associated vibrational entropy changes, making them suitable for inclusion in free energy calculations.

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Citations

Sep 10, 2011·Bioinformatics·Iain H MoalPaul A Bates
May 15, 2012·Journal of Structural Biology·Hussein M EzzeldinSantiago D Solares
Sep 26, 2015·Journal of Molecular Graphics & Modelling·Summer KassemKhaled H Barakat
Oct 3, 2013·Langmuir : the ACS Journal of Surfaces and Colloids·Stéphanie DevineauJean Philippe Renault
Mar 13, 2008·Biopolymers·D Gomika Udugamasooriya, Mark R Spaller
Jul 23, 2016·Journal of Molecular Recognition : JMR·Mark AgostinoJuan Fernández-Recio
Jun 20, 2006·Journal of Biomolecular Structure & Dynamics·Pemra DorukerOzge Kurkcuoglu
Mar 16, 2021·Physical Biology·Yves-Henri Sanejouand
Mar 16, 2021·Journal of Molecular Modeling·Anderson Aparecido do Espírito Santo, Gustavo Troiano Feliciano
Aug 27, 2010·Journal of Chemical Information and Modeling·An GhyselsVeronique Van Speybroeck
Sep 22, 2020·Journal of Chemical Information and Modeling·Arghya ChakravortyRichard H Henchman
Sep 18, 2020·Journal of Chemical Information and Modeling·Xiaocong WangJun Gao

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