Question: How To Perform Peptide-Protein Docking
gravatar for Free Man
5.4 years ago by
Free Man170
Earth - China
Free Man170 wrote:

Hi, could anybody give me an example about how to perform peptide-protein docking: the software and steps?
Here is my problem:
(1) a peptide about 10 amino acids
(2) target protein (an enzyme with known PDB structure file, and known active sites)
(3) how to find the most reliable binding site and the complex structure? (also need result like free energy)
Thank you!!!

molecular docking • 3.9k views
ADD COMMENTlink modified 2.1 years ago by Petr Ponomarenko2.6k • written 5.4 years ago by Free Man170
gravatar for João Rodrigues
5.4 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

You didn't really search Pubmed right?


  1. Get a structure of your peptide (make it in PyMOL)
  2. Get a structure of your protein (xtal, NMR, model)
  3. Use a docking program like the above.
ADD COMMENTlink written 5.4 years ago by João Rodrigues2.5k
gravatar for Woa
5.4 years ago by
United States
Woa2.7k wrote:

Not all Docking Software are good for protein-peptide docking. You can try ICM-DOCK(commercial) or AutoDOCK for that purpose. Rosetta might contain a module too.

ADD COMMENTlink written 5.4 years ago by Woa2.7k

AutoDock is a protein-ligand software, I would bet on more specific protein-peptide or protein-protein interactions. You also have FlexPepDock as an alternative.

ADD REPLYlink written 5.4 years ago by João Rodrigues2.5k

I use PatchDock to preform such docking

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by roy.granit790
gravatar for Petr Ponomarenko
2.1 years ago by
United States / Los Angeles /
Petr Ponomarenko2.6k wrote:

I use ICM-Pro from for such studies.

1) read a lot about protein family to which belongs protein of your interest and its interactions with ligand, peptides and other proteins. Is your protein a monomer, multimeter, multisubunit complex when it interacts with the peptide.

2) read a lot about domains of your protein, find which are important for this peptide binding, try to find this domains PDB structures maybe in other proteins (usually you first study domains, actually, not proteins).

3) study 3D structure properties like potential binding sites.

4) know well what you are modeling and what for. This will define your statistic function. Decide on acceptable sensitivity and specificity of your table (or you might want to optimize for AUC or something else). Know well what you are using for such modeling. Most of the software uses free energy prediction optimized for a particular task like protein folding or ligand binding, etc. Some even have multiple "free energies" for different tasks.

ADD COMMENTlink modified 2.0 years ago • written 2.1 years ago by Petr Ponomarenko2.6k
gravatar for bfmosquera1
2.1 years ago by
bfmosquera10 wrote:

Hello. I am going to work with mutant receptors. So how I can determinate if the mutant receptor will cease to binding to natural ligand? What variables should I analyze?

ADD COMMENTlink written 2.1 years ago by bfmosquera10

It is a long story =) In short, you can measure Gibbs free energy, but from good science perspective you need to study the pocket and how it interacts with different ligands and your ligand in particular.

ADD REPLYlink written 2.0 years ago by Petr Ponomarenko2.6k
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