1. Consensus RAPDF rTAD Refinement Successes & Failures Jeremy Horst Ram Samudrala’s CompBio Group University of Washington

2. Derive interatomic distances Nonredundant structure set Atom type Distance bin Bayesian probabilities Consensus RAPDF rTAD Refinement J.Horst & R.Samudrala

3. 2.11  1.46 aRMSD 0.87  0.91 GDT-TS J.Horst & R.Samudrala Consensus RAPDF rTAD Refinement - RESULTS TR488 2.94  3.51 aaRMSD 0.61  0.68 GDT-TS TR464

4. Consensus RAPDF rTAD Refinement – SIDE CHAIN PACKING J.Horst & R.Samudrala

5. CASP8R Perks + no focus on specific regions; automated + never much worse (454) CASP8 FM targets Perks + absolute best on 5/96 targets (407,409,414,455,510) + always better than 2 nd best initial model (on ~all servers)

6. Needs - Larger loop search space (looser/less constraints) - De-constrain problem areas (Seq vs. Str entropy) - Functional sites (?functional refinement target?) Advice  Benchmark on past CASPs(in papers)  Do not avoid hard targets(show limits)  Expensive methods should be iteratable  Combine Methods  Focus physics based methods here.  We need a new way to move atoms (according to Nicolay Grishin)  Are heuristics and regression / SVM okay?

7. Acknowledgements Folks who wrote code Ram Samudrala Tianyun Liu Charles Mader Ling-Hong Hung Idea bouncers ++ Michal Guerquin Brady Bernard Weerayuth Kittichotirat Stewart Moughon