GalaxyRefine: protein structure refinement driven by side-chain repacking

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

(2013) Hasup Lee et al.   BIOINFORMATICS

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

(2013) Debswapna Bhattacharya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

(2012) Junsu Ko et al.   BMC BIOINFORMATICS

GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains

(2012) Woong-Hee Shin et al.   Journal of Chemical Information and Modeling

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

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

GalaxyWEB server for protein structure prediction and refinement

(2012) J. Ko et al.   NUCLEIC ACIDS RESEARCH

The FALC-Loop web server for protein loop modeling

(2011) J. Ko et al.   NUCLEIC ACIDS RESEARCH

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

CASP9 results compared to those of previous casp experiments

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP9 assessment of free modeling target predictions

(2011) Lisa Kinch 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

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

(2011) Jian Zhang et al.   STRUCTURE

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

(2010) Ambrish Roy et al.   Nature Protocols

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

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

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of CASP8 structure predictions for template free targets

(2009) Moshe Ben-David 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

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY