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FM Model Assessment: Old scores and New Combinations

FM Model Assessment: Old scores and New Combinations. ShuoYong Shi Nick Grishin Lab. Scores used in CASP5 Assessment* : Ten scores encompass structure and sequence characteristics. GDT Distance DALI Qdali CE Qce Mammoth Qmm LGA Qlga SOV. Generate Scores.

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FM Model Assessment: Old scores and New Combinations

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  1. FM Model Assessment: Old scores and New Combinations ShuoYong Shi Nick Grishin Lab

  2. Scores used in CASP5 Assessment*:Ten scoresencompass structure and sequencecharacteristics GDT Distance DALI Qdali CE Qce Mammoth Qmm LGA Qlga SOV Generate Scores Q ratios: Correctly aligned residues/ target length *Kinch LN, et al. Proteins. 2003; 53 Suppl 6:395-409

  3. Structure Score Distributions: Target 531 GDT Dali Distance Mammoth

  4. Structure Score Distributions: Target 531 GDT Dali 399_5 113_1 360_4 Distance Mammoth 113_2 119_1 215_1 399_5

  5. Sequence Score Distributions: Target 531 Qlga Qdali 1_3 399_5 SOV Qmm 55_1 208_2

  6. Bad Score Distributions: Target 531 CE Qce

  7. Replace Score Distributions: Target 531 CE Qce Tmalign Qtm 113_4 490_2

  8. Combine Ten Scores: TenS • Strategy to combine scores: • Transform raw scores to Z-scores • 2) Sum of Z-scores using equal weight (TenS) • Throw out zeros, calculate Z-score • Throw out raw score with Z-score<-2, recalculate mean and std • Recalculate Z-score on entire population, and assign Z-score <-2 to -2.

  9. Combine Scores (TenS): Target 531 GDT winner: TS399_5 TenS winner: TS208_2 GDT TenS

  10. Combine Main Scores: TenS, QCS, GDT, and CS Score Used in Components Raw Form TenS new 10 (GDT) Z score QCS new 6 (CS) % Max GDT CASP* % Max CS CASP8 % Max Strategy to combine scores: 1) Transform raw scores to Z-scores 2) Sum of Z-scores for each target (ComS)

  11. Additional Score: Comparison to top server Model Motivation: Top performing groups use similar strategies that rank server models with various scoring functions and refine top picks Who did better than servers? Score Strategy: Ratio of best group model scores to top server model for each of the main scores

  12. Additional Score: Comparison to top server Model • Server Ratio Score Combinations: • Ratio scores below 1 are ignored • Average Scores(4) for each target • Sum score averages The Sum of average ratios (which are rarely much larger than 1) indicates the number of times each group outperformed servers

  13. Additional Score: Comparison to top server Model (Target 531 Example) Top Servers

  14. Additional Score: Comparison to top server Model (Combined Scores) Outperformed servers 14 times Servers

  15. Report Scores: Many, Many, Many Sortable Tables and a Web Site http://prodata.swmed.edu/CASP9/evaluation/CASP9Home.htm

  16. Report Scores: Many, Many, Many Sortable Tables and a Web Site

  17. Report Scores: Many, Many, Many Sortable Tables and a Web Site

  18. Report Scores: Many, Many, Many Sortable Tables and a Web Site

  19. Report Scores: Many, Many, Many Sortable Tables and a Web Site What’s the final ranking?

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