> Mensur, are you aware of any benchmark analysis that shows RAPPER's > superiority on loop modeling over MODELLER? I am aware of one that compares > Rosetta, MODELLER and CABS on loops up to 24 aa if I remember correctly, and > shows that in short lengths all 3 programs are equivalent, but for longer > loops the combination of MODELLER with CABS prevails. > > I have several proteins with missing regions of varying length (8-47 aa) > which I want to fold. I have tried PyRosetta and MODELLER in the past but > I'm not impressed from the results of loop modeling, especially as the > length increases. I guess these routines were designed to model flexible > animo acid stretches that's why the predicted conformations adopt coiled > coils. To this end I also tried I-TASSER server (which employs Monte Carlo > with Replica Exchange for regions with no templates and is questionably more > accurate in folding long aa stretches) by supplying my initial structure and > excluding all homologues, but the meta-threading program (LOMETS) it > implements always detects traces of "homology" to some irrelevant structures > and uses them as templates. I guess my last resort is MD with Replica > Exchange but I haven't found the time yet to set up my system and figure out > a way to keep the rest of the model rigid, namely to fold only the missing > regions. > > This message is slightly off-topic, but I just wanted to share my > experience (and desperation) with other people that might find it helpful (I > hope not the desperation). > > * I meant I-TASSER is ARGUABLY more accurate in folding long aa stretches.