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

Validating Resolution Revolution

(2018) Piotr Neumann et al.   STRUCTURE

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

Ionic scattering factors of atoms that compose biological molecules

(2018) Koji Yonekura et al.   IUCrJ

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy

(2017) Agnel Praveen Joseph et al.   JOURNAL OF STRUCTURAL BIOLOGY

Accurate model annotation of a near-atomic resolution cryo-EM map

(2017) Corey F. Hryc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

(2017) Jasmine Y. Young et al.   STRUCTURE

Model-based local density sharpening of cryo-EM maps

(2017) Arjen J Jakobi et al.   eLife

Responses to`Atomic resolution': a badly abused term in structural biology

(2017) Wah Chiu et al.   Acta Crystallographica Section D-Structural Biology

`Atomic resolution': a badly abused term in structural biology

(2017) Alexander Wlodawer et al.   Acta Crystallographica Section D-Structural Biology

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

(2017) Pavel Afanasyev et al.   IUCrJ

The integrative role of cryo electron microscopy in molecular and cellular structural biology

(2016) Igor Orlov et al.   BIOLOGY OF THE CELL

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage

(2016) Grigore Pintilie et al.   BIOPHYSICAL JOURNAL

Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator

(2016) Zhe Zhang et al.   CELL

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

(2016) Alan Merk et al.   CELL

Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution

(2016) Thi Hoang Duong Nguyen et al.   NATURE

On the interpretation of electron microscopic maps of biological macromolecules

(2016) Jimin Wang et al.   PROTEIN SCIENCE

Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism

(2016) J. R. Whicher et al.   SCIENCE

Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein

(2016) Francesca Coscia et al.   Scientific Reports

Validating maps from single particle electron cryomicroscopy

(2015) Peter B Rosenthal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Atomic structure of the APC/C and its mechanism of protein ubiquitination

(2015) Leifu Chang et al.   NATURE

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

(2015) Benjamin A Barad et al.   NATURE METHODS

FEM: feature-enhanced map

(2015) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

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

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Metrics for comparison of crystallographic maps

(2014) Alexandre Urzhumtsev et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

On effective and optical resolutions of diffraction data sets

(2013) Ludmila Urzhumtseva et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Bulk-solvent and overall scaling revisited: faster calculations, improved results

(2013) P. V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

How good are my data and what is the resolution?

(2013) Philip R. Evans 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

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

Finding trimeric HIV-1 envelope glycoproteins in random noise

(2013) M. van Heel   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Subramaniam, van Heel, and Henderson: Validity of the cryo-electron microscopy structures of the HIV-1 envelope glycoprotein complex

(2013) Y. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of trimeric HIV-1 envelope glycoproteins

(2013) S. Subramaniam   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise

(2013) R. Henderson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein structural ensembles are revealed by redefining X-ray electron density noise

(2013) P. T. Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Implementing an X-ray validation pipeline for the Protein Data Bank

(2012) Swanand Gore et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Statistical quality indicators for electron-density maps

(2012) Ian J. Tickle   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

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

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

(2010) Pavel V. Afonine et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Evolution of New Enzymatic Function by Structural Modulation of Cysteine Reactivity inPseudomonas fluorescensIsocyanide Hydratase

(2010) Mahadevan Lakshminarasimhan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

EMDataBank.org: unified data resource for CryoEM

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

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

(2010) P. Therese Lang et al.   PROTEIN SCIENCE

Definition and Estimation of Resolution in Single-Particle Reconstructions

(2010) Hstau Y. Liao et al.   STRUCTURE

Confidence intervals for fitting of atomic models into low-resolution densities

(2009) Niels Volkmann   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Crystallographic model quality at a glance

(2009) Ludmila Urzhumtseva 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

A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions

(2008) P. Andrew Karplus et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY