text: user6199: 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?
  
  user73: 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
  
original_text: 6199: <p>I have extracted residue 45 to 88 from a PDB file (<strong><a href="https://www.rcsb.org/structure/2yrq" rel="nofollow noreferrer">2YRQ</a></strong>).
  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.</p>
  <p>My question is what's the best way to dock it. I'm considering <strong><a href="http://vina.scripps.edu" rel="nofollow noreferrer">Autodock Vina</a></strong>.
  But I'm not sure if it's appropriate since it is for ligand-protein docking.</p>
  <p>What's the definition of a ligand? Can a protein with only 42 residues be considered a ligand?</p>
   73: <p>Answer from @pippo1980, converted from comment:</p>
  <p><a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208" rel="nofollow noreferrer">https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208</a> Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes</p>
  