Abstract
ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.
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Acknowledgements
This research has been supported by the NIH (grant number R01 GM62612). Part of this work has been performed under coordination of the EU BIOXHIT FW6 Integrated Project (grant number: LSHG-CT-2003-503420). S.X.C. thanks NWO/CW (VENT 700.55.405).
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ARP/wARP version 7 is available to all users and free of charge for academic users. Commercial users or academic users that wish to use the software for commercial research can obtain a license from EMBLEM GMBH (http://www.embl-em.de) for a fee. EMBL, NKI and all authors receive financial support from that activity according to internal rules and regulations. All authors feel that the present publication is describing scientific facts and results in a manner that is not intended to promote the use of the program, and intends only to assist the user community and provide a scientific resource for the described protocol.
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Langer, G., Cohen, S., Lamzin, V. et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3, 1171–1179 (2008). https://doi.org/10.1038/nprot.2008.91
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DOI: https://doi.org/10.1038/nprot.2008.91
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