Developing a molecular dynamics force field for both folded and disordered protein states

Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation

(2016) Erik W. Martin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2016) Jing Huang et al.   NATURE METHODS

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

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

p15PAF Is an Intrinsically Disordered Protein with Nonrandom Structural Preferences at Sites of Interaction with Other Proteins

(2014) Alfredo De Biasio et al.   BIOPHYSICAL JOURNAL

High Accuracy of Karplus Equations for Relating Three-Bond J Couplings to Protein Backbone Torsion Angles

(2014) Fang Li et al.   CHEMPHYSCHEM

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

Determination of the Individual Roles of the Linker Residues in the Interdomain Motions of Calmodulin Using NMR Chemical Shifts

(2014) Predrag Kukic et al.   JOURNAL OF MOLECULAR BIOLOGY

Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L

(2014) Fan Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

(2014) Binchen Mao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2

(2014) Yann G.J. Sterckx et al.   STRUCTURE

Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4

(2013) Paul Robustelli et al.   Journal of Chemical Theory and Computation

Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions

(2013) Vytautas Iešmantavičius et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determination of Secondary Structure Populations in Disordered States of Proteins Using Nuclear Magnetic Resonance Chemical Shifts

(2012) Carlo Camilloni et al.   BIOCHEMISTRY

Residue-Specific α-Helix Propensities from Molecular Simulation

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

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

Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies

(2012) Paul S. Nerenberg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution

(2012) Valéry Ozenne et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

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

Intrinsic disorder in measles virus nucleocapsids

(2011) M. R. Jensen 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

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

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

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

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

(2010) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

(2010) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Space of Flexible Biological Macromolecules from Average Data

(2010) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin Ligase

(2010) Tanja Mittag et al.   STRUCTURE

Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

(2009) Joseph A. Marsh et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Crystal Structure of a Ten-Amino Acid Protein

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

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

(2007) Nikola Trbovic et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS