Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Structure of the Type VI Secretion System Contractile Sheath

(2015) Mikhail Kudryashev et al.   CELL

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

(2015) Frank DiMaio et al.   NATURE METHODS

De novo protein structure determination from near-atomic-resolution cryo-EM maps

(2015) Ray Yu-Ruei Wang et al.   NATURE METHODS

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

(2015) Ryan N Jackson et al.   Nature Protocols

2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy

(2015) Melody G Campbell et al.   eLife

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome

(2014) Israel S. Fernández et al.   CELL

Structure of  -galactosidase at 3.2-A resolution obtained by cryo-electron microscopy

(2014) A. Bartesaghi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the large ribosomal subunit from human mitochondria

(2014) A. Brown et al.   SCIENCE

Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector

(2014) Matteo Allegretti et al.   eLife

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

(2013) Maofu Liao et al.   NATURE

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

(2013) Xueming Li et al.   NATURE METHODS

Cryo-EM model validation using independent map reconstructions

(2013) Frank DiMaio et al.   PROTEIN SCIENCE

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

(2013) Xiao-chen Bai et al.   eLife

Use of knowledge-based restraints inphenix.refineto improve macromolecular refinement at low resolution

(2012) Jeffrey J. Headd et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

(2010) Daniel Ting et al.   PLoS Computational Biology

X-ray structure determination at low resolution

(2009) Axel T. Brunger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

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

Oxidative challenges sensitize the capsaicin receptor by covalent cysteine modification

(2009) H.-h. Chuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Structural Correlations from Maximum Likelihood Superpositions

(2008) Douglas L. Theobald et al.   PLoS Computational Biology