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

Overview

Journal Nat Protoc

Specialties Biology
Pathology
Science

Date 2008 Jul 5

PMID 18600222

Citations 1006

Authors

Gerrit Langer

Serge X Cohen

Victor S Lamzin

Anastassis Perrakis

Affiliations

Soon will be listed here.

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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