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

D Liebschner, PV Afonine, ML Baker… - … Section D: Structural …, 2019 - journals.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods
to determine three-dimensional macromolecular structures, which are required to …

[PDF][PDF] Implications of AlphaFold2 for crystallographic phasing by molecular replacement

AJ McCoy, MD Sammito, RJ Read - Acta Crystallographica Section …, 2022 - journals.iucr.org
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction
(CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein …

[PDF][PDF] Towards automated crystallographic structure refinement with phenix. refine

PV Afonine, RW Grosse-Kunstleve… - … Section D: Biological …, 2012 - journals.iucr.org
phenix. refine is a program within the PHENIX package that supports crystallographic
structure refinement against experimental data with a wide range of upper resolution limits …

MolProbity: more and better reference data for improved all‐atom structure validation

CJ Williams, JJ Headd, NW Moriarty… - Protein …, 2018 - Wiley Online Library
This paper describes the current update on macromolecular model validation services that
are provided at the MolProbity website, emphasizing changes and additions since the …

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

PD Adams, PV Afonine, G Bunkóczi… - … Section D: Biological …, 2010 - journals.iucr.org
Macromolecular X-ray crystallography is routinely applied to understand biological
processes at a molecular level. However, significant time and effort are still required to solve …

[PDF][PDF] Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

TC Terwilliger, PD Adams, RJ Read… - … Section D: Biological …, 2009 - journals.iucr.org
Estimates of the quality of experimental maps are important in many stages of structure
determination of macromolecules. Map quality is defined here as the correlation between a …

[PDF][PDF] Automated map sharpening by maximization of detail and connectivity

TC Terwilliger, OV Sobolev, PV Afonine… - … Section D: Structural …, 2018 - journals.iucr.org
An algorithm for automatic map sharpening is presented that is based on optimization of the
detail and connectivity of the sharpened map. The detail in the map is reflected in the …

[PDF][PDF] KAMO: towards automated data processing for microcrystals

K Yamashita, K Hirata, M Yamamoto - … Crystallographica Section D …, 2018 - journals.iucr.org
In protein microcrystallography, radiation damage often hampers complete and high-
resolution data collection from a single crystal, even under cryogenic conditions. One …

A new generation of crystallographic validation tools for the protein data bank

RJ Read, PD Adams, WB Arendall, AT Brunger… - Structure, 2011 - cell.com
This report presents the conclusions of the X-ray Validation Task Force of the worldwide
Protein Data Bank (PDB). The PDB has expanded massively since current criteria for …

Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle

KHG Verschueren, C Blanchet, J Felix, A Dansercoer… - Nature, 2019 - nature.com
Across different kingdoms of life, ATP citrate lyase (ACLY, also known as ACL) catalyses the
ATP-dependent and coenzyme A (CoA)-dependent conversion of citrate, a metabolic …