Overview of the CCP4 suite and current developments

By Martyn D. Winn, C. Ballard, Kevin Cowtan, E. Dodson, P. Emsley, Philip R. Evans, Ronan M. Keegan, Eugene Krissinel, A. Leslie, A. McCoy and 8 more. 2011

11,349 citations recorded by the source corpus.

An overview of the CCP4 software suite for macromolecular crystallography is given.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Materials Chemistry

In Molecular Biology

In Computational Biology & Bioinformatics

In Computational Chemistry & Drug Discovery

Citations in the corpus

Robust deep learning based protein sequence design using ProteinMPNN (2022, methodology): “Images were integrated using XDS 20220110 (27), with Aimless (28) used for scaling and merging.”
Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “Molecular Replacement was carried out using the CCP4 package 46 via CCP4 Cloud 47 and specifically the programs Phaser 45 and MOLREP.”
Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “The rigid body refinement with REFMAC5 was followed by restrain refinement with REFMAC5, as implemented in CCP4 and Phenix.refine (93).”
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “It is also possible to obtain coordinate error predictions for other models by including them in the ensemble; methods applying this approach are sometimes referred to as quasi-single.”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “Multiple input files can be given simultaneously, e.g. a SCALEPACK file (Otwinowski & Minor, 1997) with observed intensities, a CNS (Brünger et al., 1998) file with Rfree flags (Brünger, 1992, 1993) and an MTZ file (Winn et al., 2011) with phase information.”
Improvement of molecular-replacement models with Sculptor (2011, methodology): “These algorithms have since been implemented in the CCP4 (Winn et al., 2011) programs CHAINSAW (Stein, 2008) and MOLREP (Vagin & Teplyakov, 2010).”
High‐accuracy protein structure prediction in CASP14 (2021, methodology): “The modifications made to AMPLE are now available through CCP4.”
Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor. (2018, methodology): “…TRCN0000033260 MISSION pLKO.1 luciferase shRNA control Sigma Cat# SHC007 Software and Algorithms KinTek Explorer Chemical Kinetics Software KinTek https://kintekcorp.com/software/ CCP4 software for crystallography Winn et al., 2011 http://www.ccp4.ac.uk/ QIAGEN Biomedical Genomics Workbench v4.”
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, positive): “Data from a single crystal were indexed and integrated in XDS (Kabsch, 2010) and merged using AIMLESS in CCP4 (Winn et al., 2011) (Table S1).”
How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans (2017, methodology): “The sites and phases were determined using the SHELXC/D/E pipeline in CCP4i using intensities (34).”