When a docking assignment of a ligand-receptor pair ends, AutoDock vina will output the top few best binding models and their predicted binding affinities, as shown in Figure 1. With such information, we ranked the GPCRs by the affinities between them and the input ligand, which could be retrieved from the second column titled as affinity in Figure 1. The smaller the affinity, the higher it ranks. User will receive a result of all GPCRs in a ranked list with affinity values.
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After a running session is done, our system will generate a directory including all output files and a URL link for downloading this directory will be sent to the user simultaneously. The output files contain all predicted binding models in pdbqt format, log files in txt format, and a rank list of all the GPCRs to the compound affinities between all GPCRs in our dataset and the user-defined compound.
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