Modeling the mechanism of CLN025 beta-hairpin formation

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

(2014) Robert D. Malmstrom et al.   Journal of Chemical Theory and Computation

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

Identification of slow molecular order parameters for Markov model construction

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

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Raising the Speed Limit for β-Hairpin Formation

(2012) Caitlin M. Davis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin

(2012) Søren Enemark et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

(2012) Fan Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

(2011) Bettina G. Keller et al.   CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

Exploring the Folding Free Energy Landscape of a β-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method

(2011) Ryuhei Harada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

(2011) F. Noe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

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

Psi4: an open-source ab initio electronic structure program

(2011) Justin M. Turney et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Influence of Side Chain Conformations on Local Conformational Features of Amino Acids and Implication for Force Field Development

(2010) Fan Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

(2009) Vincent Voelz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations

(2009) Lipi Thukral et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combining experiment and simulation in protein folding: closing the gap for small model systems

(2008) R Dustin Schaeffer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Folding mechanisms of individual β-hairpins in a Gō model of Pin1 WW domain by all-atom molecular dynamics simulations

(2008) Zhonglin Luo et al.   JOURNAL OF CHEMICAL PHYSICS

Crystal Structure of a Ten-Amino Acid Protein

(2008) Shinya Honda et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY