I am working with Protein-Protein docking. After docking can i apply MM-PBSA (Molecular Mechanics- Poisson Boltzmann Surface Area) calculations to the complex so formed for estimating binding energy of complex.
Generally MM-PBSA calculations are used for finding binding energy of protein-small ligand complex. Please can you help me solve my confusion.
Hi Sunil
Yes you can use it after generating trajectory. You can use single trajectory (MD run of complex only and define receptor and ligand residue during MMPBSA calculation) when no significant comformational changes occurs after ligand binding to receptor or triple trajectory (do MD simulation of complex, receptor and ligand separately) when large confirmational changes occur during after binding of ligand to receptor.
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