In case of having a newly identified pocket that might be druggable, and want to test it for docking, how can I prepare the protein in that case to avoid removing water molecules that might be essential for drug binding.
I am using protein prepartion wizard in Schrodinger Maestro for protein preparation.
Dear Amr Abbas
You can use AutoPrep and deselect the 'remove water' option and submit the job to get prepared protein in a single click.
If you still feel any problems, let me know.
That can be the right choice, but avoiding keeping water molecules is the best strategy to not fall into irrelevant interaction that can potentially give wrong or not expected results.
Best option would be to set up two different parallel runs, one with water molecules within 5 Angstroms of your new pocket, and one after removing all water molecules, if computational resources are not a limitation. You could also guide your decision by performing a structural alignment of your protein with functionally similar/related proteins to see if they have a similar pocket with bound ligand. IF the identified pocket is of a known type - for example, ATP-binding, peptide binding etc., then literature on similar pockets can also be used to inform your decision. Basically, try and characterize the binding pocket based on the protein structure, function, conservation etc before setting up the docking experiments.
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