2017
DOI: 10.1002/jcc.24923
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Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins

Abstract: Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, 2011). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained (CG) and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computa… Show more

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Cited by 1 publication
(2 citation statements)
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References 65 publications
(94 reference statements)
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“…Our study demonstrates that the REST2 method is suitable for studying IDPs, as other studies have done ( Pang and Zhou, 2015 ; Rossetti et al, 2016 ; Smith et al, 2016 ; Han et al, 2017 ; Lee and Chen, 2017 ; Hicks and Zhou, 2018 ). More intriguingly, we present an example of using it to achieve efficient sampling of the IDP-protein complex, given that simulations of such systems are generally resource demanding.…”
Section: Discussionsupporting
confidence: 68%
See 1 more Smart Citation
“…Our study demonstrates that the REST2 method is suitable for studying IDPs, as other studies have done ( Pang and Zhou, 2015 ; Rossetti et al, 2016 ; Smith et al, 2016 ; Han et al, 2017 ; Lee and Chen, 2017 ; Hicks and Zhou, 2018 ). More intriguingly, we present an example of using it to achieve efficient sampling of the IDP-protein complex, given that simulations of such systems are generally resource demanding.…”
Section: Discussionsupporting
confidence: 68%
“…As an alternative, the replica exchange with solute tempering (REST) method has been developed ( Liu et al, 2005 ) and later modified in REST2 ( Wang et al, 2011 ) to improve sampling efficiency. It has been successfully applied to the conformational sampling of IDPs ( Côté et al, 2015 ; Rossetti et al, 2016 ; Smith et al, 2016 ; Han et al, 2017 ; Lee and Chen, 2017 ; Hicks and Zhou, 2018 ). REST2 is a new form of Hamiltonian replica exchange method wherein all replicas are simulated at the same temperature T 0 albeit on different deformed potential energy surfaces.…”
Section: Introductionmentioning
confidence: 99%