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How to create a native file for Protein-Protein docking

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How to create a native file for Protein-Protein docking



We are trying to dock two proteins, let say protein A and protein B. From tutorials (, 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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Fri, 2020-06-19 08:58


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.




Mon, 2020-06-22 13:20

Thank you so much Mr. Shourya.

Mon, 2020-06-22 16:19