Prediction of CASP6 structures using automated Robetta protocols

The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. Robetta is a publicly available protein structure prediction server (http://robetta. bakerlab.org/) that uses the Rosetta de novo and homology modeling structure prediction methods. We incorporated some of the lessons learned in the CASP5 experiment into the server prior to participating in CASP6. We additionally tested new ideas that were amenable to full-automation with an eye toward improving the server. We find that the Robetta server shows the greatest promise for the more challenging targets. The most significant finding from CASP5, that automated protocols can be roughly comparable in ability with the better human-intervention predictors, is repeated here in CASP6.