While carrying protein-ligand docking can someone please tell me what are the chances of getting to the global minimum or at least close to it with Avogadro. And in totality does molecular mechanics methods solve the purpose or any other quantum mechanical approach is needed while preparing the ligands for docking?
The chances of getting a global minimum (for the ligand geometry) depend mostly on the starting point of your minimization. I haven't used Avogardo, but I'm guessing it's using one of the most popular minimization algorithms (steepest descent, conjugate gradient) which do good job as long as you're close to the true global minimum. If you want to be precise, you should definitely run some kind of conformational search.
Be aware, however, that ligand bound to the protein is not necessarily in it's global minimum geometry - the interaction with the protein almost always changes the gometry of the ligand, sometimes to a large extent.
The chances of getting a global minimum (for the ligand geometry) depend mostly on the starting point of your minimization. I haven't used Avogardo, but I'm guessing it's using one of the most popular minimization algorithms (steepest descent, conjugate gradient) which do good job as long as you're close to the true global minimum. If you want to be precise, you should definitely run some kind of conformational search.
Be aware, however, that ligand bound to the protein is not necessarily in it's global minimum geometry - the interaction with the protein almost always changes the gometry of the ligand, sometimes to a large extent.
Steepest descent often gets stuck on a slope. On the contrary, conjugate gradients almost always reaches a local minimum in the molecular-mechanical tasks.
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