CERES: a cryo-EM re-refinement system for continuous improvement of deposited models

‘We need a people’s cryo-EM.’ Scientists hope to bring revolutionary microscope to the masses

(2020) Eric Hand   SCIENCE

Improvement of cryo-EM maps by density modification

(2020) Thomas C. Terwilliger et al.   NATURE METHODS

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry

(2020) Oleg V. Sobolev et al.   STRUCTURE

Density modification of cryo-EM maps

(2020) Thomas C. Terwilliger et al.   Acta Crystallographica Section D-Structural Biology

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

(2019) Thomas C. Terwilliger et al.   PROTEIN SCIENCE

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

Model validation: local diagnosis, correction and when to quit

(2018) Jane S. Richardson et al.   Acta Crystallographica Section D-Structural Biology

Automated map sharpening by maximization of detail and connectivity

(2018) Thomas C. Terwilliger et al.   Acta Crystallographica Section D-Structural Biology

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale

(2018) Jane S. Richardson et al.   JOURNAL OF STRUCTURAL BIOLOGY

New tools for the analysis and validation of cryo-EM maps and atomic models

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Validation of Structures in the Protein Data Bank

(2017) Swanand Gore et al.   STRUCTURE

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

(2016) Alan Merk et al.   CELL

A new default restraint library for the protein backbone inPhenix: a conformation-dependent geometry goes mainstream

(2016) Nigel W. Moriarty et al.   Acta Crystallographica Section D-Structural Biology

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

(2015) Benjamin A Barad et al.   NATURE METHODS

NGL Viewer: a web application for molecular visualization

(2015) Alexander S. Rose et al.   NUCLEIC ACIDS RESEARCH

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

ThePDB_REDOserver for macromolecular structure model optimization

(2014) Robbie P. Joosten et al.   IUCrJ

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining

(2014) Zbigniew Dauter et al.   IUCrJ

Model morphing and sequence assignment after molecular replacement

(2013) Thomas C. Terwilliger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus

(2013) Qing Xie et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2013) Xueming Li et al.   NATURE METHODS

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

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

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

Movies of Ice-Embedded Particles Enhance Resolution in Electron Cryo-Microscopy

(2012) Melody G. Campbell et al.   STRUCTURE

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

Features and development ofCoot

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

EMDataBank.org: unified data resource for CryoEM

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

Case-controlled structure validation

(2009) Randy J. Read et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

On the use of logarithmic scales for analysis of diffraction data

(2009) Alexandre Urzhumtsev et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty 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

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

(2009) Robbie P. Joosten et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY