Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-12-02T00:36:36.967Z
Answers.LastActivityDate: 2021-12-02T00:36:36.967Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-21T09:55:59.740Z
Comments.Text: I would advise using the term `peptide` more so than ligand, which also includes, and generally is used to refer to, `small molecules`.
Comments.UserDisplayName: Matteo Ferla
Tags: <pdb><docking><3d-structure><structural-biology>
Title: Best way to dock subset of protein PDB and definition of a ligand
ThreadText: # Best way to dock subset of protein PDB and definition of a ligand
  
  (Asked by: username_0 on 2021-06-19)
  
  I have extracted residue 45 to 88 from a PDB file (**[2YRQ](https://www.rcsb.org/structure/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](http://vina.scripps.edu)**.
  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?
  
  **Tags:** pdb, docking, 3d-structure, structural-biology
  
  > **Comments:**
  > **username_1**: I would advise using the term `peptide` more so than ligand, which also includes, and generally is used to refer to, `small molecules`.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-12-02. Score: 1
  
  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
  
  
  ---
  
  