Morris83 ha scritto:
Ops non avevo visto che c'era anche questo topic, chedo scusa. Potete chiudere allora l'altro.
Lo scopo di D@H è quello di cercare dei ligandi che interagiscano con i siti attivi degli enzimi o con le tasche idrofobiche delle proteine. Per fare questo utilizzano il programma Autodock. Più che con rosetta@home, che se non ho capito male è un programma di ripiegamento proteico, direi che è affine al FightAids@Home del WCG (infatti lo Scripps è lo stesso gruppo di ricerca del faah).
In realtà se non erro anche rosetta ha il docking.
RosettaDock
RosettaDock was added to the Rosetta software suite during the first CAPRI experiment in 2002 as the Baker laboratory's algorithm for protein-protein docking prediction.[52] In that experiment, RosettaDock made a high-accuracy prediction for the docking between streptococcal pyogenic exotoxin A and a T cell-receptor β-chain, and a medium accuracy prediction for a complex between porcine α-amylase and a camelid antibody. While the RosettaDock method only made two acceptably accurate predictions out of seven possible, this was enough to rank it seventh out of nineteen prediction methods in the first CAPRI assessment.[52]
Development of RosettaDock diverged into two branches for subsequent CAPRI rounds as Jeffrey Gray, who laid the groundwork for RosettaDock while at the University of Washington, continued working on the method in his new position at Johns Hopkins University. Members of the Baker laboratory further developed RosettaDock in Gray's absence. The two versions differed slightly in side-chain modeling, decoy selection and other areas.[32][53] Despite these differences, both the Baker and Gray methods performed well in the second CAPRI assessment, placing fifth and seventh respectively out of 30 predictor groups.[54] Jeffrey Gray's RosettaDock server is available as a free docking prediction service for non-commercial use.[55]
In October 2006, RosettaDock was integrated into Rosetta@home. The method used a fast, crude docking model phase using only the protein backbone. This was followed by a slow full-atom refinement phase in which the orientation of the two interacting proteins relative to each other, and side-chain interactions at the protein-protein interface, were simultaneously optimized to find the lowest energy conformation.[56] The vastly increased computational power afforded by the Rosetta@home network, in combination with revised "fold-tree" representations for backbone flexibility and loop modeling, made RosettaDock sixth out of 63 prediction groups in the third CAPRI assessment.[4][21]
e non mi ricordo dove ho letto del programma rosetta ligand