Alexandre Bonvin bio photo

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

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Nucleic acids docking

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Best practice guide

HADDOCK can perform docking of nucleic acids. Currently there are no tutorials focused on docking of nucleic acids into proteins, but we are working on it. The list of nucleic acid bases supported by HADDOCKis listed here. This page consists of following chapters:


Optimal settings for docking of nucleic acids

Parameter run.cns name default value optimal value
Epsilon constant for the electrostatic energy term in it0 epsilon_0 10.0 78.0
Epsilon constant for the electrostatic energy term in it1 epsilon_1 10.0 78.0

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


Any more questions about nucleic acids 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.