Hello,
Is there a way to efficiently calculate free binding energies using MM-GBSA of a large protein/nucleic acid system? I’m talking specifically about a ribosome 60S unit (~200,000 atoms). We are interested in small molecule ligands binding at a specific site in the ribosome, and the ligand has interactions with both the RNA and a ribosomal protein. If using MM-GBSA is not feasible (because computationally limiting), what other methods are appropriate to calculate free energies for such system? Thanks!
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Received on Wed Oct 07 2026 - 13:00:04 PDT
