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Nat Protoc. 2008;3(7):1171-9. doi: 10.1038/nprot.2008.91.

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

Author information

1
European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany.

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.

PMID:
18600222
PMCID:
PMC2582149
DOI:
10.1038/nprot.2008.91
[Indexed for MEDLINE]
Free PMC Article

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