Does Rosetta have a homology modeling protocol like SWISS-MODEL or MODELLER? I couldn’t find it in source code.
I want to predict the structure of a sequence and then do a protein-protein docking, need I use MODELLER to create the structure from sequence and template pdb before repacking or loop modeling using Rosetta?
Generally, homology modeling is done using the standard abrelax tools, where you use a fragment set derived from homologs, and/or generate part of the starting structure using a homolog.
1. “where you use a fragment set derived from homologs, and/or generate part of the starting structure using a homolog”
How to generate part of the starting structure based on a homolog using Rosetta?
2. The identity between target sequence and template sequence is greater than 85%, is there any other FAST way to generate structures using Rosetta?
Having never done this, (and having had no luck so far in getting the necessary documentation), I’m just guessing.
You should be able to get a new structure from an old structure by changing the sequence to match (with fixbb, for example) and running the relax protocol. Threading gaps/insertions into the loops can be done with looprelax instead. I’m sure there are faster ways to do this but I don’t know what they are.
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