Hello everyone,
I am under a project on Protein design. I have generated a database of sequences with some programming. Now i am unable to figure out how to select sequences which will fold into the native structure. Please Please point me towards how to proceed.
I also tried homology based approach but the sequences are alot alike. Please ask if i am not making myself clear.
Will really be grateful.
As I understand your question, you have generated multiple sequence for one given backbone structure, and you want to know now how much each amino acid contributes to the folding energy of that structure.
Actually, the program you used to assign your sequence should not only generate a total score for each sequence, but also be able to break this down into the contribution of each residue to this total score. e.g. Rosetta (https://www.rosettacommons.org) will attach the per residue scores to the end of the pub files generated, you can also run models generated in other programs through rosetta "score" and get their total and per-residue scores, broken down by the different terms of the rosetta energy function.
Swarup-- You are not completely clear, but as I understand it you want to check a set of sequences against a native (known) structure. Of course I agree with Annemarie, you should use Rosetta. My lab has created a front-end for Rosetta called InteractiveRosetta, which may make it easier to calculate the energies of your sequences. For more information google "InteractiveRosetta github".
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