i have found a PDB for my research but unable to identify docking site for a particular ligand because there is no co-crystalized ligand present in protein. please provide me a way to find ligand docking site on pdb
If you have some mechanistic information about the function of your protein of interest, this might include insights into the amino acid residues that are involved in the binding of ligands (for receptors) or the binding of substrates or inhibitors (for enzymes).
Alternatively, if you have access to software, such as MOE or the Schrodinger suite, these programs have modules for predicting active sites of receptors or enzymes.
Another option is to carry out "blind docking" by encompassing the entire protein in the simulation cell. If it is a very large protein or one with multiple subunits, you can partition the protein into smaller volumes for carrying out blind docking. Sites that have favorable docking scores and that have a relatively large number of poses might include the active site as well as potential allosteric modulatory sites.
Aman Mourya Hi
If ligand is not available in your interested protein so first of all you have to study about experimental article of that protein and screen out the reactive amino acids. And other way you can go on prosite https://prosite.expasy.org/ and submit PDB ID, it will show region of active sites.
Waseem Ahmad Ansari thank you for suggestion, i have gone through experimental article already, i will try through the prosite link shared.
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