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

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

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
Open this paper in CoChat — free account

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.

Overview

Integrity signals

Registry

Crossref · 10.1021/ar000033j

Cites

61 of 61 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 29

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

Cited by

Sorted by citations

See all 4,978

Related

See all

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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review