You are here

Does Rosetta have homology modeling protocol?

4 posts / 0 new
Last post
Does Rosetta have homology modeling protocol?
#1

Hi all,

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?

Thanks.

Post Situation: 
Thu, 2010-11-04 07:36
SunH

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.

Fri, 2010-11-05 08:15
smlewis

To smlewis, thanks for your reply.

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?

Fri, 2010-11-05 11:31
SunH

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.

Mon, 2010-11-08 06:52
smlewis