I am doing some research with a drug (chemical structure is known). I am suspecting couple of binding proteins but not sure which one of them is most possible one that drug binds to. It is a kind of blind docking and I am seeking to find a lead through it, thanks.
Hey. If you are trying to dock the drug to a protein receptor for which the native ligand or known inhibitor is available with the protein structure on the pdb database, you can simply refer to the paper and get the interacting residues and plot the binding sites. You can then check if your investigational candidate is getting docked at the site. This can be done with both the protein receptors.
Alternatively, you can first dock the known inhibitor or native ligand with the protein receptor and get the interacting residues.
There are some online servers and standalone platforms like Site map, AutoSite, AutoGrid which are freely available that will help you map all the possible active binding sites on a protein. You can compare the amino acids from these binding sites and those interacting with native ligand and find out the exact amino acid composition of the binding site of the protein receptor.
Hope it helps.
Hey. If you are trying to dock the drug to a protein receptor for which the native ligand or known inhibitor is available with the protein structure on the pdb database, you can simply refer to the paper and get the interacting residues and plot the binding sites. You can then check if your investigational candidate is getting docked at the site. This can be done with both the protein receptors.
Alternatively, you can first dock the known inhibitor or native ligand with the protein receptor and get the interacting residues.
There are some online servers and standalone platforms like Site map, AutoSite, AutoGrid which are freely available that will help you map all the possible active binding sites on a protein. You can compare the amino acids from these binding sites and those interacting with native ligand and find out the exact amino acid composition of the binding site of the protein receptor.
Hope it helps.
Calculate the protein-ligand binding free energies for each query protein: the lower the protein-ligand binding free energy, the stronger the preference of the ligand for the protein.
If you get your proteins (if available from such platforms as pdb), review the interactions they are having with the ligands they originally have on pdb then you can use tools such as discovery studio, auto dock etc - for open access or Schrodinger if you have access to remove the ligands the proteins have and use your compound as ligand instead and compare the binding sites, amino acids, cavity spaces and binding energies. You will be good to go with small energies. I am not very good in this but I am perfecting my skills as well but it works for me that way.
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