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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

Peter A. KollmanDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, The Scripps Research Institute, LaJolla, California 92037, and Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112Irina MassovaUniversity of California, San FranciscoCarolina ReyesUniversity of California, San FranciscoBernd KuhnUniversity of UtahShuanghong HuoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, The Scripps Research Institute, LaJolla, California 92037, and Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112Lillian T. ChongDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, The Scripps Research Institute, LaJolla, California 92037, and Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112Matthew LeeUniversity of California, San FranciscoTai‐Sung LeeUniversity of UtahYong DuanDepartment of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, The Scripps Research Institute, LaJolla, California 92037, and Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112Wei WangUniversity of California, San FranciscoOreola DoniniUniversity of California, San FranciscoPiotr CieplakUniversity of California, San FranciscoJaysharee SrinivasanUniversity of California, San FranciscoDavid A. CaseUniversity of UtahThomas E. CheathamUniversity of Utah

2000en

ABI

Annotatsiya

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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DOI: 10.1021/ar000033j

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