Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
Peter A. Kollman(Scripps Research Institute), Irina Massova(Scripps Research Institute), Carolina Reyes(University of California, San Francisco), Bernd Kuhn(Scripps Research Institute), Shuanghong Huo(University of California, San Francisco), Lillian T. Chong(Scripps Research Institute), Matthew Lee(University of Utah), Tai‐Sung Lee(University of California, San Francisco), Yong Duan(University of California, San Francisco), Wei Wang(University of California, San Francisco), Oreola Donini(University of California, San Francisco), Piotr Cieplak(University of California, San Francisco), Jaysharee Srinivasan(Scripps Research Institute), David A. Case(Scripps Research Institute), Thomas E. Cheatham(University of Utah)
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Abstract
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein-ligand, protein-protein, and protein-nucleic acid interactions.
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