What is ADDock?

An anchored dependent molecular docking method designated as ADDock is on service now.

ADDock counts the molecular topology based on anchors chosen for building molecular structures for docking small flexible molecules or ligands into rigid active sites of protein receptors. ADDock employs an extended version of piecewise linear potential for scoring the docked structures. Since no translational motion for small molecules is implemented during the docking process, ADDock searches the best docking result by systematically changing the anchors chosen, which are usually the single-edge connected nodes or terminal hydrogen atoms of ligands. ADDock takes intact ligand structures generated during the docking process for computing the docked scores thereby no energy minimization is required in the evaluation phase of docking.

 

The docking accuracy by ADDock on 92 receptor-ligand complexes docked is 91.3%.

All these complexes have been docked by other groups using other docking methods. The good and bad docking results given by ADDock for some random ligands selected and docked into the active site of a non-native receptor are apparently separated. The discriminative ability offered by ADDock is solely based on the steric interaction energies computed between the docked structures and the receptor active site.

 

ADDock: An anchor-dependent molecular docking process for flexible small molecules inside rigid protein active sites, has been published in Journal of Chemical Information and Modeling (JCIM) .