Consensus RAPDF rTAD Refinement Successes & Failures Jeremy Horst Ram Samudrala’s CompBio...

Consensus RAPDF rTAD RefinementSuccesses & Failures

Jeremy Horst

Ram Samudrala’s CompBio GroupUniversity of Washington

Derive interatomic distancesNonredundant structure set

Atom type

Ato

m t

ype

Distance bin

Bayesian probabilitiesConsensus RAPDF rTAD Refinement

J.Horst & R.Samudrala

2.111.46 aRMSD0.870.91 GDT-TS

J.Horst & R.Samudrala

Consensus RAPDF rTAD Refinement - RESULTS

TR488

2.943.51 aaRMSD0.610.68 GDT-TS

TR464

Consensus RAPDF rTAD Refinement – SIDE CHAIN PACKING

J.Horst & R.Samudrala

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

2nd best initial model (on ~all servers)

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?

Acknowledgements

Folks who wrote code• Ram Samudrala• Tianyun Liu• Charles Mader• Ling-Hong Hung

Idea bouncers ++• Michal Guerquin• Brady Bernard• Weerayuth Kittichotirat• Stewart Moughon