Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Improved protein structure refinement guided by deep learning based accuracy estimation

(2021) Naozumi Hiranuma et al.   Nature Communications

Adaptive Cartesian and torsional restraints for interactive model rebuilding

(2021) Tristan Ian Croll et al.   Acta Crystallographica Section D-Structural Biology

EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart

(2021) Shashank Hambarde et al.   MOLECULAR CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Assessing the utility of CASP14 models for molecular replacement

(2021) Claudia Millán et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

(2021) Airlie J. McCoy et al.   Acta Crystallographica Section D-Structural Biology

Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation

(2020) Zijun Chen et al.   Advanced Science

Evaluation of template‐based modeling in CASP13

(2019) Tristan I. Croll et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

How BamA recruits OMP substrates via poly-POTRAs domain

(2019) Xiaodan Ma et al.   FASEB JOURNAL

Factors influencing estimates of coordinate error for molecular replacement

(2019) Kaushik S. Hatti et al.   Acta Crystallographica Section D-Structural Biology

On the application of the expected log-likelihood gain to decision making in molecular replacement

(2018) Robert D. Oeffner et al.   Acta Crystallographica Section D-Structural Biology

Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement

(2015) Gábor Bunkóczi et al.   STRUCTURE

Macromolecularab initiophasing enforcing secondary and tertiary structure

(2015) Claudia Millán et al.   IUCrJ

Extending molecular-replacement solutions withSHELXE

(2013) Andrea Thorn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels

(2012) Jaclyn Bibby et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Presenting your structures: theCCP4mgmolecular-graphics software

(2011) S. McNicholas et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

X-ray Crystal Structure of the UCS Domain-Containing UNC-45 Myosin Chaperone from Drosophila melanogaster

(2011) Chi F. Lee et al.   STRUCTURE

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography

(2009) Leonardo G. Trabuco et al.   METHODS