Testing gafolder
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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

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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


Testing gafolder

From David Arndt


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


New old

New / Old


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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