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

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models,10.1021/ar000033j,Accounts of Chemi

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models   (Citations: 377)
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Peter A. Kollman, Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, Oreola Donini, Piotr Cieplakhttp://academic.research.microsoft.com/io.ashx?type=5&id=10504576&selfId1=0&selfId2=0&maxNumber=12&query=
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent develop- ments 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 dynam- ics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein- ligand, protein-protein, and protein-nucleic acid interactions.
Journal: Accounts of Chemical Research - ACCOUNT CHEM RES , vol. 33, no. 12, pp. 889-897, 2000
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