The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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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“Methods such as MM-PBSA and MM-GBSA,46,47 which are based on molecular dynamics (MD) simulations, offer an alternative route for computing the binding free energies of protein–protein systems48−50 including coiled-coil complexes.42,51,52”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [46]
In the citing paper
“Previous methods were limited either in terms of their throughput (21,22) or in terms of their performance (23).”
From mCSM-PPI2: predicting the effects of mutations on protein–protein interactions (2019) · cites this paper as [21]
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The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
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g_mmpbsa —A GROMACS Tool for High-Throughput MM-PBSA Calculations
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Metadata
- 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
- 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
- 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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