I have a question about drug design based on some residues of a protein. Bear with me since I have no training in computational drug design or anything related.
I have identified some residues of a protein by a simulation method, and I would like to know how to design high specificity drug, presumably a ligand, to target these residues. What I have is the protein structure as a pdb file. I would like to know how I should proceed with this, for example, parameters that are crucial for the design, what software or algorithms can be useful for analysing the binding affinity, and probably some statistical analysis based on the ensemble?
Looking forward to your ideas, and thank you very much for your time.