Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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Peptide docking

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Best practice guide

HADDOCK supports docking of peptides as well. Since the secondary structure of short peptides is not always well defined, is is safer to dock an ensemble of multiple conformations. Different ways of generating of these conformations are described here. More documentation about peptide docking with HADDOCK is in following sections:


  • HADDOCKing of the p53 N-terminal peptide to MDM2: This tutorial introduces protein-peptide docking using the HADDOCK web server. It also introduces the CPORT web server for interface prediction, based on evolutionary conservation and other biophysical properties.


Optimal settings for docking of peptides

Parameter run.cns name default value optimal value
Clustering method clust_meth FCC RMSD
Cutoff for clustering clust_cutoff 0.6 5
Number of MD steps for rigid body high temperature TAD initiosteps 500 2000
Number of MD steps during first rigid body cooling stage cool1_steps 500 2000
Number of MD steps during second cooling stage with flexible side-chains at interface cool2_steps 500 4000
Number of MD steps during third cooling stage with fully flexible interface cool3_steps 500 4000

More about optimal settings for different docking scenarios can be found here.


Any more questions about peptide docking with HADDOCK? Have a look at our HADDOCK bioexcel forum hosted by . There is a very high chance that your problem has already been addressed.