Assessment of the model refinement category in CASP12

A Simple and Efficient Protein Structure Refinement Method

(2017) Qianyi Cheng et al.   Journal of Chemical Theory and Computation

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

(2017) Gyu Rie Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

What makes it difficult to refine protein models further via molecular dynamics simulations?

(2017) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Advances in free-energy-based simulations of protein folding and ligand binding

(2016) Alberto Perez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems

(2016) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Assessment of refinement of template-based models in CASP11

(2016) Vivek Modi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP11 statistics and the prediction center evaluation system

(2016) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein structure refinement with adaptively restrained homologous replicas

(2015) Dennis Della Corte et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP11 refinement experiments with ROSETTA

(2015) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure refinement via molecular-dynamics simulations: What works and what does not?

(2015) Michael Feig et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effective protein model structure refinement by loop modeling and overall relaxation

(2015) Gyu Rie Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

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

Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines

(2013) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

(2013) Vahid Mirjalili 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

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

(2012) Vahid Mirjalili et al.   Journal of Chemical Theory and Computation

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

An automatic method for CASP9 free modeling structure prediction assessment

(2011) Qian Cong et al.   BIOINFORMATICS

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

(2011) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Refinement of protein termini in template-based modeling using conformational space annealing

(2011) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND 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

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Assessment of the protein-structure refinement category in CASP8

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

Are Current Molecular Dynamics Force Fields too Helical?

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

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE