I wanted to pick your brains. I am using KIC with fragments to modell a loop. I am under the impression that this protocol outperfromrs the next generation KIC. Could you confirm this for me and perhap refer me to the relevant paper? Is the KIC with fragment protocol better?
Alternatively, can I use the KIC with fragments protocol with the flags from next generation KIC?
Lastly, I wanted to ask whether the KIC with fragments and Floopy Tail protocols take into the account the waters. Are these run in the explicit solvent?
Thank you very much for your help!
Here is a summary of loop modeling up to NGK: https://guybrush.ucsf.edu/benchmarks/benchmarks/loop_modeling
I don't have the KIC with fragments paper handy but agree I have heard it is supposed to be better. https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/loop_modeling/KIC_with_fragments Look for a paper that Roland Pache is on, I guess.
No Rosetta protocols use explicit water except those that are made for the purpose (which you can probably tell from their name). FloppyTail and loop modeling are not made for explicit water. Having a limited number of explicit waters as ligands might work.
Do you know wheather I can use KIC with fragments protocol with the flags fro NGK?
I'm not aware of any reason you can't. I don't have any insight you won't get from the Kortemme lab documentation.