3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

Assessment of protein structure refinement in CASP9

(2011) Justin L. MacCallum 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

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

(2010) Z. Wang et al.   BIOINFORMATICS

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

MolProbity: all-atom structure validation for macromolecular crystallography

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

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

(2009) Yunqi Li et al.   PLoS One

Assessment of the protein-structure refinement category in CASP8

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

The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models

(2009) Daniel A. Keedy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved prediction of protein side-chain conformations with SCWRL4

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

Evaluation of template-based models in CASP8 with standard measures

(2009) Domenico Cozzetto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

(2008) Qiang Wang et al.   Nature Protocols

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

Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities

(2008) El-Ad David Amir et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A multi-template combination algorithm for protein comparative modeling

(2008) Jianlin Cheng   BMC STRUCTURAL BIOLOGY