Please refer to the following link. Hope u find it useful: https://www.researchgate.net/post/How_to_find_binding_energy_between_two_proteins

This is a vast topic and tools are only useful to a skilled hand. Acceptability of the docking result does not depend on the software; any software is equally capable of producing garbage.

If it is a small peptide, any docking program can handle the docking. If it is a large peptide, then the choice becomes limited. Further, if your large peptide does not have a crystal structure docking is almost useless. You can generate a model of the peptide and then some initial guess of the complex by docking. However, molecular dynamics simulation is recommended on all those guess structures of the complexes.

Dear Devanshu

For protein peptide docking you can use web server like haddock. https://milou.science.uu.nl/services/HADDOCK2.2/haddock.php

or stand alone version of haddock or hex.

While the binding energy is a relative term and depends on the force field and parameters you are using.

Most import point is to identify the relevant binding pockets in the protein, where there is possibility of peptide binding and the flexible residues should be considered as an parameter in protein while docking peptides.

As Uttam suggested, try to perform MD of the complex, to get more accurate picture of protein peptide docking.

Thank you Rajesh, Uttam, and Tanuj for the inputs.

Before docking, it is better to collect more literatures for support, so that the simulation results are not empty, to ensure the accuracy of docking. The relatively famous software today is Hex Protein Docking, ZDock, rDock, and Rosetta, etc. Among them, Hex Protein Docking is more complicated, but it has no scoring function. ZDock is generally used as the initial docking of the previous period, and rDock is the upgrading algorithm of ZDock.

Hope it helps!