In their third benchmark competition, over one dozen proteins were designed to bind a steroid. Can you determine which were successful? (timeframe: 1 month and ends on 26 April 2013). See www.CSARdock.org to download the zip file.
This exercise is built around designed proteins developed by Tinberg, Khare, and Baker. This is an interesting twist on traditional docking/scoring problems because there is no existing protein data on which to train models (as was possible in the first two exercises). Three phases, with a possible fourth phase are coming up:
Phase 1: Protein design – Over one dozen proteins were designed to bind a steroid. Can you determine which were successful? (timeframe: 1 month, ending 26 April 2013)
Phase 2: Scoring – Given the set-up crystal structures of the proteins and a set of pregenerated docking decoys, can you identify the correct poses for the steroid? (timeframe: start after Phase 1 ends and run 2 weeks)
Phase 3: Selectivity – Given the set-up crystal structures of some protein-steroid complexes, can you predict the binding affinity (or relative ranking) of several steroids binding to the same protein? (timeframe: start after Phase 2 ends and run 1 month)
Phase 4: Predict the effect of protein mutations – There is extensive mutational data available. Given a subset, can you "bin" their effects into weak, moderate, significant changes in binding? (timeframe: longer and not yet determined)