CHARMM36m: an improved force field for folded and intrinsically disordered proteins

CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State

(2016) Sander Boonstra et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

(2015) Aaron M. Fluitt et al.   BIOPHYSICAL JOURNAL

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

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data

(2015) Athanasios S. Baltzis et al.   PROTEIN SCIENCE

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

(2014) Po-chia Chen et al.   BIOPHYSICAL JOURNAL

Single-Molecule Studies of Intrinsically Disordered Proteins

(2014) Marco Brucale et al.   CHEMICAL REVIEWS

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

(2014) Karl T. Debiec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Testing the validity of ensemble descriptions of intrinsically disordered proteins

(2014) M. R. Jensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

(2014) Alexey B. Mantsyzov et al.   PROTEIN SCIENCE

Automated Optimization of Potential Parameters

(2013) Michele Di Pierro et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Systematic Improvement of a Classical Molecular Model of Water

(2013) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2012) Peter Eastman 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

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Charge interactions can dominate the dimensions of intrinsically disordered proteins

(2010) S. Muller-Spath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CHARMM: The biomolecular simulation program

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

Examining Polyglutamine Peptide Length: A Connection between Collapsed Conformations and Increased Aggregation

(2009) Robert H. Walters et al.   JOURNAL OF MOLECULAR BIOLOGY

Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein

(2009) Wenli Meng et al.   PROTEIN SCIENCE

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation