D3Docking was developed with two functions based on protein structure based docking, one is for predicting drug targets for drugs or active compounds observed from clinic or in vitro/vivo studies, the other is for screening lead compounds against drug targets via molecular docking. For improving success rate, we collected and constructed the three-dimensional structures of different conformations of the potential target proteins, and predicted their druggable conformations as many as reasonable by using NUMD and vsREMD developed by our lab. D3Pockets, which was also developed by our lab, was then applied to predict potential ligand-binding sites for each protein conformation. “TargetPrediction” is for predicting target proteins, while “VirtualScreening” is for molecular docking against multiple ligand-binding sites of a specific or multiple target proteins.
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