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 score Energy = w 1 x s 1 + w 2 x s 2 + … 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. PDBRMSD (Å)MIN (Å)MAX (Å)AVG (Å)STD 1A2P 2.461.15 / 1.442.25 / 2.461.71 / 2.120.35 / 0.28 1B79 2.62.3 / 2.86.42 / 3.083.18 / 2.921.09 / 0.08 1DFU 2.651.02 / 0.942.53 / 2.121.43 / 1.260.47 / 0.32 1I1J 3.983.44 / 3.684.09 / 4.053.78 / 3.870.21 / 0.1 1IG5 1.431.17 / 1.421.54 / 1.561.37 / 1.480.1 / 0.04 1RCB 4.863.25 / 11.3 21.92 / 20.6715.75 / 15.89 5.1 / 3.29 1W41 2.763.3 / 2.286.77 / 9.434.44 / 5.131.08 / 2.01 2CI2 1.830.73 / 1.041.7 / 6.691.31 / 1.840.34 / 1.62 2D3D 2.21.34 / 1.92 2.41 / 15.46 1.81 / 3.490.3 / 3.99 6PTI 3.20.83 / 0.951.62 / 1.571.03 / 1.250.22 / 0.16 1UBQ(1) 1.381.09 / 1.21.7 / 1.561.27 / 1.320.16 / 0.09 1UBQ(2) 2.451.61 / 1.862.21 / 2.161.84 / 1.960.16 / 0.09 New / Old

9. Complete results http://www.cs.ualberta.ca/~jianjun/prio n/gafolder/

10. Acknowledgments Dr. Wishart Dr. Lin Alberta Prion Institute NSERC David Arndt Mark Berjanskii Paul Lu Cam Macdonell Steve Sutphen