We<i> present improved Monte Carlo statistical mechanics methods for modeling proteins and protein-ligand complexes with emphasis on the motions of the protein backbone and side chains. Comparisons are made with conformational sampling by molecular dynamics for 18 dipeptides and T4 lysozyme L99A. The performance of the improved MC algorithms is further evaluated by computing absolute free energies of binding for L99A lysozyme with eight benzene analogs and for inhibitors of macrophage migration inhibitory factor (MIF). With proper protein sampling, similar results are obtained using MC and MD, while significant advantages in computation speed are found with MC.</i>

Enhanced Monte Carlo methods for proteins and computation of absolute free energies of binding

256th National Meeting (2018)

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