I am currently looking for any tools to analyze the probable docking sites intead of going for blind docking. Is there any bio-informatics tools or webserver that can help me further analyze the pockets present in my protein of interest and export the co-ordinates.
Here are some popular tools you can consider:
It is important to carefully analyze the results from these tools and consider using multiple tools to cross-validate the predicted binding sites.
Hi Sambit Mandi,
First, you should try to find out the ligand binding pocket of a protein from the reported literature, from here you can get the significant residues for efficient ligand binding and generate the grid box.
Secondly, if there is no literature evidence present, you can use an online tool like CASTp ( http://sts.bioe.uic.edu/castp/ ) and others as mentioned above to get the details of binding pocket residues.
Next, you can generate the coordinates of this probable binding pocket using AutoDock Tool and also be able to export your grid dimensions file.
