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ACORN: a review.

J X Yao1, E J Dodson, K S Wilson

  • 1York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, England. yao@ysbl.york.ac.uk

Acta Crystallographica. Section D, Biological Crystallography
|July 21, 2006
PubMed
Summary
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The ACORN system now solves protein structures using less than atomic resolution data. New methods improve density modification, enabling high-quality maps even with limited data.

Area of Science:

  • * Structural biology
  • * Crystallography
  • * Computational biology

Background:

  • * The ACORN system was developed for ab initio protein structure solution using atomic resolution data.
  • * Initial phase determination is crucial and can be derived from structural fragments.
  • * Iterative refinement involves dynamic density modification (DDM) and Sayre-equation refinement (SER).

Observation:

  • * ACORN has been enhanced to solve protein structures with sub-atomic resolution data.
  • * Artificial data extension to 1 Å resolution is a key development.
  • * Low-resolution maps previously showed poor C-atom visibility, especially C(alpha) atoms.

Findings:

  • * New density modification (DDM1, DDM2) and enhancement (ENH) procedures improve low-resolution maps.

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  • * High-quality, atom-specific maps are now achievable with limited diffraction data.
  • * ACORN effectively refines phase sets from anomalous scattering and isomorphous derivative data.

    • Implications:

    • * Enables protein structure determination with less ideal crystallographic data.
    • * Advances automated interpretation of electron density maps.
    • * Broadens the applicability of ACORN to a wider range of structural biology problems.