How to create a native file for Protein-Protein docking

[Anonymous]

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.

[Anonymous]

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:

1. The order of the chains is the same as in the input, and
2. The same number of residues are present in the input and native.

 

Best,

Shourya

[Anonymous]

Thank you so much Mr. Shourya.

[Author]

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