Randomizing side chain orientation of a protein structure
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5.6 years ago

Hello,

I have the quaternary structures of hetero-dimeric proteins. I am trying to separate the 2 chains of each protein complex and dock them. Prior to docking I have to randomize the side chain orientation of all amino acids in both the chains of each of the protein complexes.

Is there any software that can randomize the side chain orientations of all amino acids in a protein in a single command?

Thank you in advance

Akash

Protein structure Rotamer Side chain orientation • 1.4k views
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I don't know much but I think thermodynamical minimum energy structure is some what different from biological structure.

As in normal protein ligand docking validation people take out ligand minimise it then dock it again to check if it achieve conformation closer to its biological conformation.

So you can minimise the both chain individual and I hope it must be sufficient. And I also hope I am not pointing u in wrong direction.

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Thank you! I have heard that the biological structure as found in a PDB file need not necessarily be the structure of least energy. My question is would just a minimization of the energies of both chains be sufficient to randomize all of the surface side chains? I want to remove any native-complex bias that the structures may have. I am using a rigid-body docking algorithm to dock the chains of various hetero-dimers. Some of them do not have unbound structures for each chain. This is why I turned to randomizing the side chain orientation of all surface residues.

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