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ARP/wARP and molecular replacement.

A Perrakis1, M Harkiolaki, K S Wilson

  • 1Department of Molecular Carcinogenesis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. perrakis@nki.nl

Acta Crystallographica. Section D, Biological Crystallography
|September 22, 2001
PubMed
Summary
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Automated model building and refinement in macromolecular crystallography is improved with ARP/wARP. This software automates tasks like autobuilding, model updating, and side-chain refinement, accelerating structure solution.

Area of Science:

  • Macromolecular crystallography
  • Structural biology
  • Computational biology

Background:

  • Refining and rebuilding initial models after molecular replacement is often time-consuming.
  • Automated methods are needed to improve the efficiency of crystallographic model building.

Purpose of the Study:

  • To present ARP/wARP as a tool for automating model building and refinement in macromolecular crystallography.
  • To demonstrate the utility of ARP/wARP in accelerating structure solution and improving crystallographic maps.

Main Methods:

  • ARP/wARP offers automated model building from molecular replacement phases.
  • It provides options for updating existing models via atom addition/deletion.
  • The software facilitates docking structures to new sequences followed by real-space side-chain refinement.

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Main Results:

  • ARP/wARP significantly speeds up structure solution in several cases.
  • The software enables refinement of difficult or uninterpretable crystallographic maps.
  • Complete protein structure autobuilding is feasible at resolutions of 2.0 Å and better.
  • Map improvement using ARP/wARP shows advantages over conventional refinement even at 3.2 Å.

Conclusions:

  • ARP/wARP enhances automation in macromolecular crystallography model building and refinement.
  • The tool offers flexible options for different stages of structure analysis.
  • ARP/wARP demonstrably improves efficiency and success rates in solving and refining crystal structures.