Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

Simulating rare events using a weighted ensemble-based string method

(2013) Joshua L. Adelman et al.   JOURNAL OF CHEMICAL PHYSICS

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

(2012) Victor Ovchinnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unrestrained Computation of Free Energy along a Path

(2012) Bradley M. Dickson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences

(2012) Victor Ovchinnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations

(2012) Serdal Kirmizialtin et al.   STRUCTURE

Stereochemical errors and their implications for molecular dynamics simulations

(2011) Eduard Schreiner et al.   BMC BIOINFORMATICS

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

(2011) Victor Ovchinnikov et al.   JOURNAL OF CHEMICAL PHYSICS

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Antiparallel EmrE exports drugs by exchanging between asymmetric structures

(2011) Emma A. Morrison et al.   NATURE

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Conformational Free-Energy Difference of a Miniprotein from Nonequilibrium Simulations

(2010) Martin Spichty et al.   Journal of Physical Chemistry Letters

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis

(2010) Andrei A. Golosov et al.   STRUCTURE

Nonequilibrium umbrella sampling in spaces of many order parameters

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Exact rate calculations by trajectory parallelization and tilting

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Separating forward and backward pathways in nonequilibrium umbrella sampling

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions

(2009) He Huang et al.   Journal of Chemical Theory and Computation

Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials

(2009) Luca Maragliano et al.   Journal of Chemical Theory and Computation

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers

(2009) M. Cecchini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mapping the Network of Pathways of CO Diffusion in Myoglobin

(2009) Luca Maragliano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of two distinct inactive conformations of the  2-adrenergic receptor reconciles structural and biochemical observations

(2009) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Eckart axis conditions, Gauss’ principle of least constraint, and the optimal superposition of molecular structures

(2008) Gerald R. Kneller   JOURNAL OF CHEMICAL PHYSICS

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY