Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Optimal Superpositioning of Flexible Molecule Ensembles

(2013) Vytautas Gapsys et al.   BIOPHYSICAL JOURNAL

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow

(2013) Igor V. Kalgin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Separability between overall and internal motion: A protein folding problem

(2013) Eric Johnson   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On Reaction Coordinate Optimality

(2012) Sergei V. Krivov   Journal of Chemical Theory and Computation

Identifying Metastable States of Folding Proteins

(2012) Abhinav Jain et al.   Journal of Chemical Theory and Computation

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

(2012) Cristian Micheletti   Physics of Life Reviews

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Normal mode analysis of protein dynamics in a non-Eckart frame

(2010) Sotaro Fuchigami et al.   JOURNAL OF CHEMICAL PHYSICS

Latent dynamics of a protein molecule observed in dihedral angle space

(2010) Satoshi Omori et al.   JOURNAL OF CHEMICAL PHYSICS

Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

(2010) Abhinav Jain et al.   Journal of Physical Chemistry Letters

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Multidimensional Langevin modeling of biomolecular dynamics

(2009) Rainer Hegger et al.   JOURNAL OF CHEMICAL PHYSICS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis

(2009) Laura Riccardi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

(2009) Gia G. Maisuradze et al.   PHYSICAL REVIEW LETTERS

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

Detection of Functional Modes in Protein Dynamics

(2009) Jochen S. Hub et al.   PLoS Computational Biology

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

(2009) Lucy R. Allen et al.   PLoS Computational Biology

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

(2008) Alexandros Altis et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations

(2008) Cristian Micheletti et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Diffusive reaction dynamics on invariant free energy profiles

(2008) S. V. Krivov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding energy landscape and network dynamics of small globular proteins

(2008) N. Hori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA