Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

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

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

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein folding and de novo protein design for biotechnological applications

(2013) George A. Khoury et al.   TRENDS IN BIOTECHNOLOGY

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

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Assessment of protein structure refinement in CASP9

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

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

MolProbity: all-atom structure validation for macromolecular crystallography

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

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessment of the protein-structure refinement category in CASP8

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

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

FACTS: Fast analytical continuum treatment of solvation

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