Cited by 4,978Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsAdvanced Chemical Physics Studies

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 +7 more·2000·Accounts of Chemical Research

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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Crossref · 10.1021/ar000033j

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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
Venue
Accounts of Chemical Research
Published
2000-10-04
Volume
33
Issue
12
Pages
889-897
ISSN
  • 0001-4842 (ISSN-L)
  • 1520-4898
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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