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

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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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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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