Project Features
Contact Us

GPCR Panel Help

PDBQT files

GPCR Panel accepts the input of pdbqt. This format is very similar to pdb format but it includes partial charges ('Q') and AutoDock 4 atom types ('T'). Users can use AutoDockTools for converting pdb format to pdbqt.

For more information:
How to prepare a ligand file for AutoDock 4
What is the format of a PDBQT file?

Example files

Three example files of input compounds are available below:

Pergolide example: Pergolide PDBQT file
Plerixafor example: Plerixafor PDBQT file
Chlorpromazine example: Chlorpromazine PDBQT file

Off target prediction

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.

Exporting files

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.

GPCR Library List

5-HT1B receptor
5-HT2B receptor
A2A receptor
M2 receptor
M4 receptor
AT1 receptor
CB1 receptor
CRF1 receptor
D3 receptor
FFA1 receptor
glucagon receptor
mGlu1 receptor
mGlu5 receptor
H1 receptor
LPA1 receptor
δ receptor
κ receptor
NOP receptor
OX2 receptor
P2Y1 receptor
P2Y12 receptor
S1P1 receptor
M1 receptor
ETB receptor
OX1 receptor
A1 receptor
AT2 receptor
CT receptor
GLP-1 receptor