1 / 10

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

marion
Download Presentation

Testing GaFolder

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related