protein structure generation from sequences with IMP
Hello all,
We are working on a project in which we need to generate protein models from the amino acid sequences, using IMP. After reading on the IMP website, I can see that this tool primarily deals with different data sources. But, still I believe that this tool could be useful for us as we might need to add more information later.
Have you ever tried generating models (like pdb files) with just amino acid sequences using IMP? If you have anything that could be helpful to me please help.
Warm Regards, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54@mail.missouri.edumailto:BAP54@mail.missouri.edu
On 04/10/2012 12:40 PM, Adhikari, Badri (MU-Student) wrote: > We are working on a project in which we need to generate protein models > from the amino acid sequences, using IMP.
If you want to build extended chain structures, see http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_se...
If you have some extra knowledge (e.g. stereochemistry, atom-atom distances) you can then add that in as restraints and sample.
If you want to build homology models, IMP doesn't do that - you can use our MODELLER package to do that instead.
If you want to build ab initio models, you might want to try a tool like Rosetta.
Ben
participants (2)
-
Adhikari, Badri (MU-Student) -
Ben Webb