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Testing GaFolder. Jianjun (Benjamin) Zhou Dept. of Computing Science. Introduction to GaFolder. History …Raj Maiti, David Arndt, … Function Sub-program: potential Calculate protein structure energy Measurement of structure quality 10 (16) element scores Energy function Main-program

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testing gafolder

Testing GaFolder

Jianjun (Benjamin) Zhou

Dept. of Computing Science

introduction to gafolder
Introduction to GaFolder
  • History…Raj Maiti, David Arndt, …
  • Function
    • Sub-program: potential
      • Calculate protein structure energy
        • Measurement of structure quality
      • 10 (16) element scores
        • Energy function
    • Main-program
      • Refine protein structures
        • Genetic algorithm
training testing potential
Training & Testing Potential
  • Components of potential scoreEnergy = w1 x s1 + w2 x s2 + …
  • Training method
    • Linear regression + Manual adjustment
    • Weka
      • Free
      • Multi-platform
        • Windows, Linux, Mac
      • Graphic interface, command line
  • Training & Testing data
    • CASP7
      • 91 proteins, 91 x 500 decoys
    • Other decoy sets
      • Rosetta, …
results on potential
Results on Potential
  • High accuracy: 80/90 (89%) within 2.5Å
  • Well scaled: lowest energy [-5, -10]
results on structure refinement
Results on Structure Refinement
  • Testing data
    • 11 proteins
    • Distorted Structure: randomly varying all phi and psi angles uniformly within ±5°.
  • SOP
    • Generate 10 copies of GaFolder
    • For each input structure, minimize it concurrently on 10 GaFolders
    • Return 10 minimized structures
comparison on two versions of gafolder
Comparison on Two Versions of GaFolder
  • Version 1: v124
    • Incorporated the Shiftx code into GaFolder
  • Version 2: Mark’s revision
    • Shiftx is called outside GaFolder
complete results
Complete results
  • http://www.cs.ualberta.ca/~jianjun/prion/gafolder/
acknowledgments
Acknowledgments
  • Dr. WishartDr. Lin
  • Alberta Prion InstituteNSERC
  • David ArndtMark Berjanskii
  • Paul LuCam Macdonell Steve Sutphen
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