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Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG. CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:1079-1089. [PMID: 36048148 PMCID: PMC9435598 DOI: 10.1107/s2059798322007987] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
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 to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.
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Affiliation(s)
- Eugene Krissinel
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Andrey A. Lebedev
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Ville Uski
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Charles B. Ballard
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Ronan M. Keegan
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Oleg Kovalevskiy
- Scientific Computing Department, Science and Technology Facilities Council UK, Didcot OX11 0FA, United Kingdom
| | - Robert A. Nicholls
- Structural Studies Division, MRC Laboratory for Structural Biology, Cambridge CB2 0QH, United Kingdom
| | - Navraj S. Pannu
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Pavol Skubák
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - John Berrisford
- European Bioinformatics Institute, Hinxton CB9 1SD, United Kingdom
| | - Maria Fando
- Institute of Protein Research, Pushchino 142290, Russian Federation
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jens M. H. Thomas
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Christopher Oliver
- School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Clemens Vonrhein
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Arnaud Basle
- Newcastle University Biosciences Institute Medical School, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Andrew Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Michail N. Isupov
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Edward Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Josep Triviño
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Kevin Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Isabel Uson
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Victor Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Gerard Bricogne
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Andrew G. W. Leslie
- Structural Studies Division, MRC Laboratory for Structural Biology, Cambridge CB2 0QH, United Kingdom
| | - David G. Brown
- Servier Research Institute in Croissy-sur-Seine, 125 Chemin de Ronde, 78290 Croissy, France
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