Hi,
We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.
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Hello,
Firstly, it is not compulsory to include a native file to run docking. You could choose not to use a native file; it does not affect the docking algorithm in any way.
A native file is used when we want to compare the RMSD of the models to a known structure, eg. if you are trying to benchmark a protocol or if you have a homologous complex. If you have a homologous complex, I would individually align A and B to their respective homologs in the complex, say A' and B' and then save the PDB with that orientation of A-B. You could then use this PDB as your native file.
If using a native file, make sure:
Best,
Shourya
Thank you so much Mr. Shourya.