Automated Macromolecular Model Building for X-ray Crystallography Using ARP/wARP Version 7

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray / methods*
  • Ligands
  • Macromolecular Substances / chemistry*
  • Models, Molecular*
  • Proteins / chemistry*
  • Software*

Substances

  • Ligands
  • Macromolecular Substances
  • Proteins