Alexandre Bonvin bio photo

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

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Coarse grained docking

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Best practice guide

To be able to perform docking of large biological complexes in a reasonable timescale HADDOCK offers an option to coarse grain molecules. By downscaling the level of resolution of biomolecules to coarser representations HADDOCK can study protein interactions that are hardly accessible by classical atomistic approaches. Currently coarse-graining of proteins and nucleic acids with Martini is supported. Preparation of coarse-grained pdb files is described in the HADDOCK manual here and coarse grained topology is described in run.cns format in the manual here. All available documentation about coarse-graining is summed up in these sections:



Optimal settings of docking of coarse grained molecules

Parameter run.cns name default value optimal value
Dieletric constant for it0 dielec_0 rdie cdie
Dieletric constant for it1 dielec_1 rdie cdie

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


Any more questions about coarse-grained 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.