Testing GaFolder
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Testing GaFolder Jianjun (Benjamin) Zhou Dept. of Computing Science
description
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 - PowerPoint PPT Presentation
Transcript of 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• Refine protein structures
• Genetic algorithm
From David Arndt
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
High accuracy: 80/90 (89%) within 2.5Å Well scaled: lowest energy [-5, -10]
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
Version 1: v124Incorporated the Shiftx code into
GaFolder Version 2: Mark’s revision
Shiftx is called outside GaFolder
PDB RMSD (Å) MIN (Å) MAX (Å) AVG (Å) STD
1A2P 2.46 1.15 / 1.44 2.25 / 2.46 1.71 / 2.12 0.35 / 0.28
1B79 2.6 2.3 / 2.8 6.42 / 3.08 3.18 / 2.92 1.09 / 0.08
1DFU 2.65 1.02 / 0.94 2.53 / 2.12 1.43 / 1.26 0.47 / 0.32
1I1J 3.98 3.44 / 3.68 4.09 / 4.05 3.78 / 3.87 0.21 / 0.1
1IG5 1.43 1.17 / 1.42 1.54 / 1.56 1.37 / 1.48 0.1 / 0.04
1RCB 4.86 3.25 / 11.3 21.92 / 20.67 15.75 / 15.89 5.1 / 3.29
1W41 2.76 3.3 / 2.28 6.77 / 9.43 4.44 / 5.13 1.08 / 2.01
2CI2 1.83 0.73 / 1.04 1.7 / 6.69 1.31 / 1.84 0.34 / 1.62
2D3D 2.2 1.34 / 1.92 2.41 / 15.46 1.81 / 3.49 0.3 / 3.99
6PTI 3.2 0.83 / 0.95 1.62 / 1.57 1.03 / 1.25 0.22 / 0.16
1UBQ(1) 1.38 1.09 / 1.2 1.7 / 1.56 1.27 / 1.32 0.16 / 0.09
1UBQ(2) 2.45 1.61 / 1.86 2.21 / 2.16 1.84 / 1.96 0.16 / 0.09
New / Old
Complete results
http://www.cs.ualberta.ca/~jianjun/prion/gafolder/
Acknowledgments
Dr. WishartDr. Lin
Alberta Prion InstituteNSERC
David ArndtMark Berjanskii
Paul LuCam Macdonell Steve Sutphen
