<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>

CC BY-SA 4.0
2021-12-02T00:36:36.967Z
2021-12-02T00:36:36.967Z
gringer
<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>

CC BY-SA 4.0
2021-06-21T09:55:59.740Z
I would advise using the term `peptide` more so than ligand, which also includes, and generally is used to refer to, `small molecules`.
Matteo Ferla
<pdb><docking><3d-structure><structural-biology>
Best way to dock subset of protein PDB and definition of a ligand
# 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`.  

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## 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


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