The DOI matches its Crossref record; 54 of the 55 references it cites were found in a registry or an index.
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
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?
In the citing paper
“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 [47]
Citations
Cites
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
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
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-citationKlamt, A., & Schüürmann, G. (1993) · Journal of the Chemical Society Perkin Transactions 2 · doi:10.1039/p29930000799 · Cited by 9,449
Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100142a004 · Cited by 8,152
Self-citationTomasi, J., & Persico, M. (1994) · Chemical Reviews · doi:10.1021/cr00031a013 · Cited by 5,530
Electric Moments of Molecules in Liquids
Onsager, L. (1936) · Journal of the American Chemical Society · doi:10.1021/ja01299a050 · Cited by 5,350
Semianalytical treatment of solvation for molecular mechanics and dynamics
Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. F. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00172a038 · Cited by 3,653
Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,891
Miertuš, S., & Tomasi, J. (1982) · Chemical Physics · doi:10.1016/0301-0104(82)85072-6 · Cited by 2,480
Flagged first, then by citations
1 of the 55 references couldn’t be matched to a known paper.
Research works printed but not linked: 4
- Born, M.Z., Phys., 1 (1920) 45.
- Debye, P. and Hückel, E., Physik. Z., 24 (1923) 185.
- Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.R., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A., AMBER4.1 (UCSF), University of California, San Francisco, CA, 1995.
- Jorgensen, W.L., BOSS3.6, Yale University, New Haven, CT, 1996.
Cited by
Sorted by citations
MMPBSA.py : An Efficient Program for End-State Free Energy Calculations
Miller, B. R., McGee, T. D., Swails, J., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300418h · Cited by 4,664
gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
Tresanco, M. S. V., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00645 · Cited by 3,468
Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00055 · Cited by 2,341
Gohlke, H., Kiel, C., & Case, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,205
Wang, R., Lai, L., & Wang, S. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1016357811882 · Cited by 1,185
Metadata
- Authors
- Massova, I., & Kollman, P. A.
- Affiliations
- University of California, San Francisco (US)
- Venue
- Perspectives in Drug Discovery and Design
- Published
- 2000-06
- Volume
- 18
- Issue
- 1
- Pages
- 113-135
- ISSN
- 0928-2866 (ISSN-L)
- 1573-9023
- OpenAlex
- W1549357029
- Cited by
- 1,015
- References
- 55
- Citations by year
- 2026: 58 · 2025: 85 · 2024: 64 · 2023: 85 · 2022: 67 · 2021: 83 · 2020: 57 · 2019: 46 · 2018: 48 · 2017: 47 · 2016: 46 · 2015: 39 · 2014: 45 · 2013: 36 · 2012: 34
- FWCI
- 10.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Perspectives in Drug Discovery and Design (publishedVersion)
- Funders
- National Institute for Health and Care Research
- National Institutes of Health
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- MM-PBSA, ligand binding prediction, binding free energy, solvent effects, solvation energy, scanning mutagenesis, molecular dynamics, high-throughput screening, binding affinity ranking
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
