The CCP4 suite: integrative software for macromolecular crystallography

J Agirre, M Atanasova, H Bagdonas… - Biological …, 2023 - journals.iucr.org
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective
with a mission to develop, test, distribute and promote software for macromolecular …

Validation of the crystallography open database using the crystallographic information framework

A Vaitkus, A Merkys, S Gražulis - Applied Crystallography, 2021 - journals.iucr.org
Data curation practices of the Crystallography Open Database (COD) are described with
additional focus being placed on the formal validation using the Crystallographic Information …

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

TI Croll - Biological Crystallography, 2018 - journals.iucr.org
This paper introduces ISOLDE, a new software package designed to provide an intuitive
environment for high-fidelity interactive remodelling/refinement of macromolecular models …

Overview of refinement procedures within REFMAC5: utilizing data from different sources

O Kovalevskiy, RA Nicholls, F Long… - Biological …, 2018 - journals.iucr.org
Refinement is a process that involves bringing into agreement the structural model,
available prior knowledge and experimental data. To achieve this, the refinement procedure …

[HTML][HTML] Electron diffraction data processing with DIALS

MTB Clabbers, T Gruene, JM Parkhurst… - Biological …, 2018 - journals.iucr.org
Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure
determination of macromolecules from three-dimensional nanometre-sized crystals. The …

findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

G Chojnowski, AJ Simpkin, DA Leonardo… - IUCrJ, 2022 - journals.iucr.org
Although experimental protein-structure determination usually targets known proteins,
chains of unknown sequence are often encountered. They can be purified from natural …

The science is in the data

JR Helliwell, B McMahon, JM Guss… - IUCrJ, 2017 - journals.iucr.org
Understanding published research results should be through one's own eyes and include
the opportunity to work with raw diffraction data to check the various decisions made in the …

[HTML][HTML] CCP4 Cloud for structure determination and project management in macromolecular crystallography

E Krissinel, AA Lebedev, V Uski, CB Ballard… - Biological …, 2022 - journals.iucr.org
Nowadays, progress in the determination of three-dimensional macromolecular structures
from diffraction images is achieved partly at the cost of increasing data volumes. This is due …

[HTML][HTML] Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

MTB Clabbers, E van Genderen, W Wan… - Biological …, 2017 - journals.iucr.org
Three-dimensional nanometre-sized crystals of macromolecules currently resist structure
elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a …

Distributed computing for macromolecular crystallography

E Krissinel, V Uski, A Lebedev, M Winn… - Biological …, 2018 - journals.iucr.org
Modern crystallographic computing is characterized by the growing role of automated
structure-solution pipelines, which represent complex expert systems utilizing a number of …