Consensus RAPDF rTAD Refinement Successes & Failures Jeremy Horst Ram Samudrala’s CompBio Group University of Washington
Dec 29, 2015
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