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

Conformational and Dynamic Changes at the Interface Contribute to Ligand Binding by Ubiquitin

(2012) Monica Sundd   BIOCHEMISTRY

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

(2012) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Intrinsic Energy Landscapes of Amino Acid Side-Chains

(2012) Xiao Zhu et al.   Journal of Chemical Information and Modeling

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp 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

Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

(2012) Kresten Lindorff-Larsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network

(2012) Lydia Nisius et al.   Nature Chemistry

Systematic Validation of Protein Force Fields against Experimental Data

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

Toward a Predictive Understanding of Slow Methyl Group Dynamics in Proteins

(2011) Dong Long et al.   BIOPHYSICAL JOURNAL

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Force field refinement from NMR scalar couplings

(2011) Jing Huang et al.   CHEMICAL PHYSICS

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

(2011) Paul S. Nerenberg et al.   Journal of Chemical Theory and Computation

Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins

(2011) Da-Wei Li et al.   Journal of Chemical Theory and Computation

A Hydrogen Bond Regulates Slow Motions in Ubiquitin by Modulating a β-Turn Flip

(2011) Arshdeep Sidhu et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing Side-Chain Dynamics in Proteins by the Measurement of Nine Deuterium Relaxation Rates Per Methyl Group

(2011) Xinli Liao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Signature of Mobile Hydrogen Bonding of Lysine Side Chains from Long-Range15N–13C ScalarJ-Couplings and Computation

(2011) Levani Zandarashvili et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

NMR-Based Protein Potentials

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

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins

(2010) Jing Huang et al.   Journal of Chemical Theory and Computation

Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear1H−15N NMR Spectroscopy

(2010) Alexandre Esadze et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accessing ns–μs side chain dynamics in ubiquitin with methyl RDCs

(2009) Christophe Farès et al.   JOURNAL OF BIOMOLECULAR NMR

CHARMM: The biomolecular simulation program

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

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

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

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics

(2008) Nils-Alexander Lakomek et al.   JOURNAL OF BIOMOLECULAR NMR

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator

(2008) Pedro E. M. Lopes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY