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

Kollman, Peter A., Massova, Irina, Reyes, Carolina, Kuhn, Bernd, Huo, Shuanghong, Chong, Lillian, Lee, Matthew, Lee, Taisung, Duan, Yong, Wang, Wei, Donini, Oreola, Cieplak, Piotr, Srinivasan, Jaysharee, Case, David A., Cheatham, Thomas E.·2000·Accounts of Chemical Research

DOI 10.1021/ar000033j

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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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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 29,638
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Computer Simulation of Liquids
P, S., & J, K. (1988) · Journal of Molecular Liquids · doi:10.1016/0167-7322(88)80022-9 · Cited by 16,088
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111
Self-citation
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
Sitkoff, D. F., Sharp, K. A., & Honig, B. H. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100058a043 · Cited by 2,160
Free energy calculations: Applications to chemical and biochemical phenomena
Kollman, P. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,101
Self-citation
Dynamics of folded proteins
McCammon, J., Gelin, B., & Karplus, M. (1977) · Nature · doi:10.1038/267585a0 · Cited by 1,972
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., & Case, D. A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja981844+ · Cited by 1,634
Self-citation
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
Duan, Y., & Kollman, P. A. (1998) · Science · doi:10.1126/science.282.5389.740 · Cited by 1,337
Self-citation
Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin
Oubridge, C., Ito, N., Evans, P. R., Teo, C.-H., & Nagai, K. (1994) · Nature · doi:10.1038/372432a0 · Cited by 832

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Research works printed but not linked: 29

Postma J. P. M., 1982, Faraday Symp. Chem. Soc.
Tembe B. L., 1984, Comput. Chem., 8, 283
Jorgensen W. L., 1985, J. Chem. Phys., 83, 3054
Cheatham T. E., 1996, J. Mol. Biol., 259, 444
Srinivasan J., 1998, J. Am. Chem. Soc., 120, 9409
Vorobjev Y. N., 1998, Funct. Genet.
Sitkoff D., 1998, J. Phys. Chem., 98, 1983
Cheatham T. E., 1998, J. Biomol. Struct. Des., 16, 280
Simmerling C., 1998, J. Am. Chem. Soc., 120, 7155
Lee M., 2000, Proteins, 39, 316
Lee M., J. Am. Chem. Soc., submitted.
Simons K. T., 1999, Funct. Genet.
Cordes M. H. J., 1999, Science, 284, 327
Kollman P. A., 1997, Computer Simulations of Biomolecular Systems: Computer Simulations of Biomolecular Systems
Kuhn B., J. Med. Chem., in press.
Wang J., 1998, Proteins, 34, 81
Wang W., 1999, Proteins, 34, 402
Kuhn B., 2000, J. Am. Chem. Soc, 122, 3916
Donini O., J. Med. Chem., in press.
Wang W., J. Mol. Biol., in press.
Reyes C., 1999, RNA, 5, 244
Avis J. M., 1996, J. Mol. Biol., 257, 341
Allain F. H. T., 1996, Nature, 380, 650
Grubser C. C., 1996, Biochemistry, 35, 2267
Dubridge C., 1994, Nature, 372, 438
Vorobjev C. Y. N., 1999, Biophys. Chem., 78, 205
Lee T., 2000, J. Am. Chem. Soc., 122, 4393
Williams D. J., 1999, Biophys. J., 76, 3205
Zou X. Q., 1999, J. Am. Chem. Soc., 121, 8043

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Authors: Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E.
Affiliations: Scripps Research Institute (US)
Department 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 84112
ORCID: Kuhn, Bernd
Huo, Shuanghong
Chong, Lillian
Duan, Yong
Wang, Wei
Donini, Oreola
Cieplak, Piotr
Case, David A.
Cheatham, Thomas E.
Venue: Accounts of Chemical Research
Publisher: American Chemical Society (ACS)
Published: 2000-10-04
Volume: 33
Issue: 12
Pages: 889-897
ISSN: 0001-4842 (ISSN-L)
1520-4898
DOI: 10.1021/ar000033j
OpenAlex: W1975580333
Cited by: 4,978
References: 61
Citations by year: 2026: 261 · 2025: 323 · 2024: 299 · 2023: 345 · 2022: 313 · 2021: 336 · 2020: 290 · 2019: 259 · 2018: 249 · 2017: 248 · 2016: 243 · 2015: 197 · 2014: 236 · 2013: 233 · 2012: 220
FWCI: 13.25
Type: journal article
Language: en
Open access: closed
Locations: Accounts of Chemical Research (publishedVersion)
PubMed (publishedVersion)
Rutgers University Community Repository (Rutgers University) (submittedVersion)
Funders: National Institutes of Health (2r01ca025644-22)
National Cancer Institute (CA25644)
National Institute of General Medical Sciences (R01GM029072, GM29072)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords: molecular dynamics, biological macromolecules, force fields, implicit solvent, relative free energy, molecular mechanics, nucleic acid duplexes, RNA hairpin, protein folding, protein-ligand interactions, protein-protein interaction, protein-nucleic acid interactions, structural calculation
MeSH terms: Base Sequence, DNA, Models, Molecular, Proteins, RNA, Thermodynamics, Molecular Structure

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

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