Effective protein model structure refinement by loop modeling and overall relaxation

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

(2014) Hahnbeom Park et al.   PLoS One

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Andriy Kryshtafovych 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

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Optimization of protein models

(2012) Dominik Gront et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

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

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

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

(2011) Jian Zhang et al.   STRUCTURE

Protein loop modeling by using fragment assembly and analytical loop closure

(2010) Julian Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Homology modeling in drug discovery: current trends and applications

(2009) Claudio N. Cavasotto et al.   DRUG DISCOVERY TODAY

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress and challenges in protein structure prediction

(2008) Yang Zhang   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

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

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