Structure Prediction Protein Design Biclustering + cMonkey Network Inference Publications          Links + Collaborations People                   Opportunities             Software + Code Teaching            

 

WCG Status Update

Answer

The side chains are missing in these pictures. BUT wait a minute ... we thought HPF2 was all-atom (including side chains). The explanation is that we perform the Rosetta search in all-atom mode (high resolution) but here we've just left off the side chains to make this annoying quiz. Also, for some applications we do the big calculation in all-atom mode and then save only the backbones of the lowest scoring structures. This saves space and if we need the side chain atoms for any reason it is very fast to put them back on with Rosetta (many thousands of times faster than the original calculation: Rosetta built the modes with side chains initially, so its very for Rosetta to get them back in the same, or nearly same, orientation given a Rosetta generates backbone and score).