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

Collaborative Computational Project for Electron cryo-Microscopy

(2015) Chris Wood 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

Finding the right fit: chiseling structures out of cryo-electron microscopy maps

(2014) Elizabeth Villa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

(2014) P. Unverdorben et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beyond blob-ology

(2014) M. T. J. Smith et al.   SCIENCE

Structure of the Yeast Mitochondrial Large Ribosomal Subunit

(2014) A. Amunts et al.   SCIENCE

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle

(2014) Christoph Leidig et al.   Nature Communications

Beam-induced motion correction for sub-megadalton cryo-EM particles

(2014) Sjors HW Scheres   eLife

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

(2014) Matteo Allegretti et al.   eLife

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

(2014) Wilson Wong et al.   eLife

Conformation-independent structural comparison of macromolecules withProSMART

(2014) Robert A. Nicholls et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions

(2013) Giovanni Cardone et al.   JOURNAL OF STRUCTURAL BIOLOGY

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

(2013) José Ramón Lopéz-Blanco et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

(2013) M. L. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cross-validation in cryo-EM-based structural modeling

(2013) B. Falkner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM model validation using independent map reconstructions

(2013) Frank DiMaio et al.   PROTEIN SCIENCE

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

(2013) A. I. Petrov et al.   RNA

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

(2013) Shaoxia Chen et al.   ULTRAMICROSCOPY

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

(2013) Xiao-chen Bai et al.   eLife

RCrane: semi-automated RNA model building

(2012) Kevin S. Keating et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

(2012) Thomas C. Terwilliger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Handling ligands withCoot

(2012) Judit É. Debreczeni et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Low-resolution refinement tools inREFMAC5

(2012) Robert A. Nicholls et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps

(2012) Matthew L. Baker et al.   BIOPOLYMERS

Real-space refinement with DireX: From global fitting to side-chain improvements

(2012) Zhe Wang et al.   BIOPOLYMERS

Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in Cryo-EM density maps

(2012) Grigore Pintilie et al.   BIOPOLYMERS

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Prevention of overfitting in cryo-EM structure determination

(2012) Sjors H W Scheres et al.   NATURE METHODS

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

(2012) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

(2011) L. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electronic detectors for electron microscopy

(2011) A. R. Faruqi et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Features and development ofCoot

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

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

Conformational change of flagellin for polymorphic supercoiling of the flagellar filament

(2010) Saori Maki-Yonekura et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

EMDataBank.org: unified data resource for CryoEM

(2010) C. L. Lawson et al.   NUCLEIC ACIDS RESEARCH

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

(2009) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Molecular replacement withMOLREP

(2009) Alexei Vagin 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

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

(2009) Frank DiMaio et al.   JOURNAL OF MOLECULAR BIOLOGY

An automated procedure for detecting protein folds from sub-nanometer resolution electron density

(2009) Reza Khayat et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural basis for translation termination on the 70S ribosome

(2008) Martin Laurberg et al.   NATURE

BPS: a database of RNA base-pair structures

(2008) Y. Xin et al.   NUCLEIC ACIDS RESEARCH

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE