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Testing GaFolder

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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  1. Testing GaFolder Jianjun (Benjamin) Zhou Dept. of Computing Science

  2. 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

  3. From David Arndt

  4. 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, …

  5. Results on Potential • High accuracy: 80/90 (89%) within 2.5Å • Well scaled: lowest energy [-5, -10]

  6. 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

  7. 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

  8. New / Old

  9. Complete results • http://www.cs.ualberta.ca/~jianjun/prion/gafolder/

  10. Acknowledgments • Dr. WishartDr. Lin • Alberta Prion InstituteNSERC • David ArndtMark Berjanskii • Paul LuCam Macdonell Steve Sutphen

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