Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

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

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

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

Assessment of protein structure refinement in CASP9

(2011) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How Fast-Folding Proteins Fold

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

Reliable protein structure refinement using a physical energy function

(2010) Matthew S. Lin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent

(2010) Srinivasaraghavan Kannan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sampling Bottlenecks in De novo Protein Structure Prediction

(2009) David E. Kim 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

Assessment of the protein-structure refinement category in CASP8

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

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations

(2008) Ryuichiro Ishitani et al.   MOLECULAR SIMULATION

Protein model refinement using an optimized physics-based all-atom force field

(2008) A. Jagielska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent dramatically affects protein structure refinement

(2008) G. Chopra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

An efficient conformational sampling method for homology modeling

(2007) Rongsheng Han et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS