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Protein modeling
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When the homology model has been build the quality must be evaluated. If the model is to be used for drug design, the prefered way of evaluation would be to mutate the residues sourounding the putative bindingsite of the ligands. If mutation of the residues expected to have favourable interactions with the ligand(s) reduces binding affinity, the model is probably predictive.
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In this example a ligand (the selective NK2 antagonist SR48968 from Sanofi) has been docked into the putative bindingsite of the homology model from the previous page. You can highlight residues experimentally determined to be important for binding of this ligand.
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Links
Molecular Mechanics (MM)
Pharmacophore Modeling
Docking
Protein Modeling
Molecular Quantum Mechanics
Physical & Chemical properties
Ph.D. Project
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