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Iterative ACORN as a high throughput tool in structural genomics.

S Selvanayagam1, D Velmurugan, T Yamane

  • 1Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.

Indian Journal of Biochemistry & Biophysics
|December 1, 2006
PubMed
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ACORN, a CCP4 program, enhances high-throughput protein structure determination by providing efficient phasing. Iterative application of ACORN, combined with ARP/wARP and REFMAC, aids in building protein models for structural genomics.

Area of Science:

  • Structural biology
  • Structural genomics
  • Computational biology

Background:

  • High-throughput macromolecular structure determination is crucial for structural genomics.
  • The volume of available sequence data significantly outpaces the number of known 3D protein structures.
  • Efficient methods are needed to accelerate the process of determining protein structures.

Purpose of the Study:

  • To present ACORN as a comprehensive and efficient program for phasing in protein structure determination.
  • To highlight the utility of ACORN in combination with other programs for high-throughput structural genomics.
  • To demonstrate the adaptability of ACORN using secondary structural elements and iterative approaches.

Main Methods:

  • Utilizing ACORN, a program within the CCP4 suite, for phasing with atomic resolution data.

Related Experiment Videos

  • Employing ACORN in conjunction with automatic model-building program ARP/wARP and refinement program REFMAC.
  • Running ACORN with secondary structural elements (helices, sheets) as input for high-resolution data.
  • Applying iterative ACORN phasing using fragments (incomplete models/dummy atoms) when initial phasing is insufficient.

    • Main Results:

    • ACORN demonstrates efficiency in phasing for protein structure determination.
    • The combination of ACORN, ARP/wARP, and REFMAC is suitable for high-throughput structural genomics.
    • ACORN can effectively utilize secondary structural elements as input with high-resolution data.
    • Iterative ACORN phasing proved efficient in subsequent model building stages for congerin and catalase.

    Conclusions:

    • ACORN is a valuable tool for accelerating protein structure determination in structural genomics.
    • The iterative application of ACORN, along with complementary software, facilitates robust model building.
    • ACORN's flexibility in input types enhances its applicability across various structural biology challenges.