High‐accuracy refinement using Rosetta in CASP13

refineD: improved protein structure refinement using machine learning based restrained relaxation

(2019) Debswapna Bhattacharya   BIOINFORMATICS

Driven to Near‐Experimental Accuracy by Refinement via Molecular Dynamics Simulations

(2019) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein homology model refinement by large-scale energy optimization

(2018) Hahnbeom Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12

(2017) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2017) Gyu Rie Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure prediction using Rosetta in CASP12

(2017) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of the model refinement category in CASP12

(2017) Ladislav Hovan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models

(2015) André Wildberg et al.   Journal of Chemical Theory and Computation

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

CASP11 refinement experiments with ROSETTA

(2015) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

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

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

Refinement of Unreliable Local Regions in Template-based Protein Models

(2012) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Modeling Symmetric Macromolecular Structures in Rosetta3

(2011) Frank DiMaio et al.   PLoS One

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

Super-resolution biomolecular crystallography with low-resolution data

(2010) Gunnar F. Schröder et al.   NATURE