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Modeller CSA based on SNUMOL Junsu Ko 2009. 8. 24. Lab. Of Compbio. SNU. InSilico 단백질 연구단

Modeller CSA based on SNUMOL Junsu Ko 2009. 8. 24. Lab. Of Compbio. SNU. InSilico 단백질 연구단. Modeller CSA. CSA. Wrapper. Tinker Chain building,. Modeller. Old Modeller CSA. 문제점 Modeller is used as a blackbox Disk I/O 가 너무 많음 . Customize 가 불가능 . CSA 성능 개선 필요 .

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Modeller CSA based on SNUMOL Junsu Ko 2009. 8. 24. Lab. Of Compbio. SNU. InSilico 단백질 연구단

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  1. Modeller CSA based on SNUMOL Junsu Ko 2009. 8. 24. Lab. Of Compbio. SNU. InSilico 단백질 연구단

  2. Modeller CSA CSA Wrapper Tinker Chain building, ... Modeller

  3. Old Modeller CSA • 문제점 • Modeller is used as a blackbox • Disk I/O 가 너무 많음. • Customize 가 불가능. • CSA 성능 개선 필요. • Initial Bank 생성, Operators, Reminimization, ....

  4. New Modeller CSA CSA CSA Based on SNUMOL Modeller Modeller Energy Function SNUMOL Library Tinker

  5. New Modeller CSA (cont.) • Modeller CSA is now based on a single, unified platform. • Disk I/O 가 없음. • Customization 이 자유로움 • Better minimization algorithm • L-BFGS-B ( Quasi-Newton ) • Modeller 8 : Conjugate Gradient • Miscellaneous improvements on the CSA part: • More opreators, reminimization, seed reset cut, etc

  6. Benchmark : Targets • CASP8 targets • GDT-TS 기준 • 10개 구간 당 1개씩 • T0388, T0398, T0424, T0427, T0430, T0436, T0489, T0451, T0473, T0486 • Zhang-Server 와 비교 • Score차이가 큰 것 11개 • T0393, T0397, T0400, T0421, T0457, T0462, T0464, T0466, T0468, T0478, T0513 • 동일한 1st bank 사용.

  7. Benchmark : Platform • New Modeller CSA(run on Compbio Cluster) • Intel Xeon E5410 Quad Core * 2 (8 core) • RAM : 16G • MAX NFT : 500 / No MD • Old Modeller CSA (run on KIAS Cluster during CASP8) • 32 CPU • MAX NFT : 200 (Modeller Default) • MD

  8. Old vs. New Modeller CSA

  9. TBM-HA

  10. TBM

  11. FM

  12. T0478 • Energy • 17807.69 → 20171.49 -2363.80 • NFT • 3,443,723 → 8,605,210

  13. T0478 : ModellerCSA 결과

  14. T0478 : Bank 1st

  15. T0478 : Templates

  16. Conclusion • Modeller CSA has been reproduced and reinforced based on SNUMOL • Efficient energy minimization with L-BFGS-B required new parameterization regarding bank update • Computation time has been reduced • Other miscellaneous points in CSA have been fixed • Reminimization, … • New implementation and energy bug fix did not lead to improved prediction in backbone or sidechain accuracy

  17. Future works • Operator 개선 • Energy 함수 개선 • First bank 개선

  18. END

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