Replica exchange with guided annealing for accelerated sampling of disordered protein conformations

Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

(2014) Weihong Zhang et al.   Journal of Chemical Theory and Computation

Enhanced exchange algorithm without detailed balance condition for replica exchange method

(2013) Hiroko X. Kondo et al.   JOURNAL OF CHEMICAL PHYSICS

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions

(2013) Weihong Zhang et al.   Journal of Chemical Theory and Computation

Towards the physical basis of how intrinsic disorder mediates protein function

(2012) Jianhan Chen   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

A convective replica-exchange method for sampling new energy basins

(2012) Yannick G. Spill et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins

(2012) Weihong Zhang et al.   PLoS Computational Biology

Velocity scaling for optimizing replica exchange molecular dynamics

(2011) Maksim Kouza et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

(2011) Michael S. Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Intrinsically Disordered Proteins in a Physics-Based World

(2010) Timothy H. Click et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Generalized Replica Exchange Method

(2010) Jaegil Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Atomistic Details of the Disordered States of KID and pKID. Implications in Coupled Binding and Folding

(2009) Debabani Ganguly et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding–unfolding equilibria

(2008) Robert Denschlag et al.   CHEMICAL PHYSICS LETTERS

Exchange frequency in replica exchange molecular dynamics

(2008) Daniel Sindhikara et al.   JOURNAL OF CHEMICAL PHYSICS

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

(2008) Hugh Nymeyer   Journal of Chemical Theory and Computation

Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding†

(2008) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding proteins by first-passage-times-optimized replica exchange

(2008) Walter Nadler et al.   PHYSICAL REVIEW E

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

(2007) Jianhan Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE