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

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

(2016) Julian von der Ecken et al.   NATURE

Assessment of refinement of template-based models in CASP11

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

2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition

(2016) S. Banerjee et al.   SCIENCE

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

(2015) Justin L. MacCallum 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

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

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

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

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

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

(2013) David E. Kim 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

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

(2012) Junsu Ko et al.   BMC BIOINFORMATICS

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

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

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Evaluation of model quality predictions in CASP9

(2011) Andriy Kryshtafovych 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

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

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