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BioDock (16, 17,18) is a docking software developed in our laboratory, which is able to produce, evaluate and classify a very high number of complexes between two interaction partners in a rapid and efficient way (about one million of trial complexes per hour). In the present version, both the compounds are kept fixed. For each compound, about 10.000.000 complexes have been screened using energetical and sterical criteria implemented in BioDock. Like showed in the following chart, the software use a stochastic approach to generate the orientations of the ligand-receptor complex. Each acceptable complex is clustered and only the best representative orientations are stored in the trajectory file. Infact, a stochastic only method produces many similar orientations without gaining new informations about the binding site.



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