Protein-ligand dock using haddock


I am working on protein-ligand docking. i have successfully completed the run but now i have a doubt on the analysis part. a) Here, i have set the number of structures to analyze as 500. and also the Number of structures for semi-flexible refinement and Number of structures for the explicit solvent refinement as 500 as well. The doubt is will the haddock server evaluate only the 500 structures or will it evaluate more number of structures and return me only top 500 structures as output?

b) What is the algorithm used by Haddock server?

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Hi Dinesh

a) is you asked for 500 models, HADDOCK can’t analyse more than that… There is also an parameter defining the number of models to analyse (those will be used in the clustering process). It is defined under the analysis parameter menu: Number of structures to analyze (the default is 200)

b) Time to do some reading… In short: Rigid-body EM, then simulated annealing using torsion angle MD and finally short MD refinement in explicit solvent.


and also several Methods in Molecular Biology chapters (listed on