Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies

(2019) Jana Ognjenović et al.   Annual Review of Biomedical Engineering

A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue

(2019) Miroslava Schaffer et al.   NATURE METHODS

Automatic local resolution-based sharpening of cryo-EM maps

(2019) Erney Ramírez-Aportela et al.   BIOINFORMATICS

Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events

(2019) Sangmi Jun et al.   PROTEIN JOURNAL

Modelling structures in cryo-EM maps

(2019) Sony Malhotra et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CENP-A nucleosome clusters form rosette-like structures around HJURP during G1

(2019) Leonid Andronov et al.   Nature Communications

3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations

(2018) Leonid Andronov et al.   BIOINFORMATICS

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

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

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

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores

(2018) Grigore Pintilie 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

Visualization of chemical modifications in the human 80S ribosome structure

(2017) S. Kundhavai Natchiar et al.   NATURE

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

High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective

(2017) Alexander Wlodawer et al.   STRUCTURE

Model-based local density sharpening of cryo-EM maps

(2017) Arjen J Jakobi et al.   eLife

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

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

On the interpretation of electron microscopic maps of biological macromolecules

(2016) Jimin Wang et al.   PROTEIN SCIENCE

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

(2015) Serban L. Ilca et al.   Nature Communications

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

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

Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy

(2015) Holger Stark et al.   Microscopy

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

(2013) Angelita Simonetti et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Likelihood-based classification of cryo-EM images using FREALIGN

(2013) Dmitry Lyumkis et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

Exploiting structure similarity in refinement: automated NCS and target-structure restraints inBUSTER

(2012) Oliver S. Smart et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

(2011) E. V. Orlova et al.   CHEMICAL REVIEWS

Features and development ofCoot

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