Experimental accuracy in protein structure refinement via molecular dynamics simulations

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

(2016) Paweł Krupa et al.   BIOINFORMATICS

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

(2016) Jing Huang et al.   NATURE METHODS

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

Evaluation of Unrestrained Replica-Exchange Simulations Using Dynamic Walkers in Temperature Space for Protein Structure Refinement

(2014) Mark A. Olson et al.   PLoS One

On the Universe of Protein Folds

(2013) Rachel Kolodny et al.   Annual Review of Biophysics

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

Assessment of the assessment: Evaluation of the model quality estimates in CASP10

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of predictions in the CASP10 model refinement category

(2013) Timothy Nugent et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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 Fast-Folding Proteins Fold

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

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

(2008) Jiang Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS