Multiscale enhanced sampling of intrinsically 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

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

(2014) Weihong Zhang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements

(2014) Sean M. Law et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer

(2013) Hiroshi Fujisaki 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

Atomistic molecular simulations of protein folding

(2012) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

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

Scalable free energy calculation of proteins via multiscale essential sampling

(2010) Kei Moritsugu et al.   JOURNAL OF CHEMICAL PHYSICS

Topology-based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions

(2010) Debabani Ganguly et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles

(2009) Patrick Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

(2008) Vladimir N. Uversky et al.   Annual Review of Biophysics

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

(2008) Robert Denschlag et al.   CHEMICAL PHYSICS LETTERS

Reconstructing atomistic detail for coarse-grained models with resolution exchange

(2008) Pu Liu et al.   JOURNAL OF CHEMICAL PHYSICS

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

Subdomain Competition, Cooperativity, and Topological Frustration in the Folding of CheY

(2008) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2002) John Karanicolas et al.   PROTEIN SCIENCE