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Literature DB >> 26606236

Improved Replica Exchange Method for Native-State Protein Sampling.

Samuel L C Moors¹, Servaas Michielssens¹, Arnout Ceulemans¹.

Abstract

We present a new replica exchange method, designed for optimal native state protein sampling in explicit solvent, called replica exchange with flexible tempering (REFT). The method was built upon the recently introduced replica exchange with solute tempering (REST). The potential function is adapted to direct the conformational search toward interdomain movements and the flexible portions of the protein. We demonstrate the improved sampling efficiency of REFT compared to the original REST for the bacteriophage T4 lysozyme.

Entities: Species

Year: 2010 PMID： 26606236 DOI： 10.1021/ct100493v

Source DB: PubMed Journal: J Chem Theory Comput ISSN： 1549-9618 Impact factor: 6.006

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Cited

11 in total

1. On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities.

Authors: Lingle Wang; B J Berne; Richard A Friesner
Journal: Proc Natl Acad Sci U S A Date: 2012-01-23 Impact factor: 11.205

2. Free energy landscape of a minimalist salt bridge model.

Authors: Xubin Li; Chao Lv; Karen M Corbett; Lianqing Zheng; Dongsheng Wu; Wei Yang
Journal: Protein Sci Date: 2015-09-02 Impact factor: 6.725

3. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

Authors: Lingle Wang; Richard A Friesner; B J Berne
Journal: J Phys Chem B Date: 2011-07-07 Impact factor: 2.991

4. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

Authors: Wei Jiang; James C Phillips; Lei Huang; Mikolai Fajer; Yilin Meng; James C Gumbart; Yun Luo; Klaus Schulten; Benoît Roux
Journal: Comput Phys Commun Date: 2014-03 Impact factor: 4.390

Review 5. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

Authors: Takaharu Mori; Naoyuki Miyashita; Wonpil Im; Michael Feig; Yuji Sugita
Journal: Biochim Biophys Acta Date: 2016-01-05

Improved Replica Exchange Method for Native-State Protein Sampling.

1. On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities.

2. Free energy landscape of a minimalist salt bridge model.

3. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

4. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

Review 5. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

6. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

7. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.

Review 8. Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins.

9. Facet selectivity in gold binding peptides: exploiting interfacial water structure.

10. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering.