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


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.

SUBMITTER: Langer G 

PROVIDER: S-EPMC2582149 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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

Langer Gerrit G   Cohen Serge X SX   Lamzin Victor S VS   Perrakis Anastassis A  

Nature protocols 20080101 7


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 hi  ...[more]

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