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I have extracted residue 45 to 88 from a PDB file (2YRQ). With that I have a new smaller PDB file. Let's call it 45_88.pdb And I want to dock it to some other full protein.

My question is what's the best way to dock it. I'm considering Autodock Vina. But I'm not sure if it's appropriate since it is for ligand-protein docking.

What's the definition of a ligand? Can a protein with only 42 residues be considered a ligand?

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    $\begingroup$ I would advise using the term peptide more so than ligand, which also includes, and generally is used to refer to, small molecules. $\endgroup$
    – Matteo Ferla
    Commented Jun 21, 2021 at 9:55

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Answer from @pippo1980, converted from comment:

https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208 Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes

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