GPCR Panel only accepts the input of file in a 3D SDF format, a popular chemical-data file format.

Three example files of input compounds are available below:

Pergolide example: Pergolide 3D SDF file
Plerixafor example: Plerixafor 3D SDF file
Chlorpromazine example: Chlorpromazine 3D SDF file

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.

Figure 1. Examples of Autodock vina outputs.

After a running session is done, our system will send the result page (URL link) to the user. The results will be ranked by the binding affinities. Visualization of docking pose is also provided with embedded NGL viewer for further inference.