BioHackersNetRosetta is one of the currently most successful ab initio methods developed by the group of David Baker
In the Rosetta method, the chain of a protein is broken into three or nine residue segments. A search in [http://www.robetta.com/fragmentqueue.jsp the fragment library] was carried out to obtain the distribution of the conformations for each target segment. Then a conformation space was built from the insertion of the segments. New improved Rosetta used a sequence and secondary structure profile-profile camparsion method to do the searching from the fragment library. And then a Monte Carlo Simulated Annealing procedure was used to select favorable structures from the conformation space with an improved energy function. Since lots of decoy structures were generated during the process, a final filtering and clustering procedure was used to select the candidates from the decoys.
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