The DOI matches its Crossref record; 79 of the 79 references it cites were found in a registry or an index.
Biophysical experiments and biomolecular simulations: A perfect match?
Abstract
A fundamental challenge in biological research is achieving an atomic-level description and mechanistic understanding of the function of biomolecules. Techniques for biomolecular simulations have undergone substantial developments, and their accuracy and scope have expanded considerably. Progress has been made through an increasingly tight integration of experiments and simulations, with experiments being used to refine simulations and simulations used to interpret experiments. Here we review the underpinnings of this progress, including methods for more efficient conformational sampling, accuracy of the physical models used, and theoretical approaches to integrate experiments and simulations. These developments are enabling detailed studies of complex biomolecular assemblies.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
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
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 7,285
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
Replica-exchange molecular dynamics method for protein folding
Sugita, Y., & Okamoto, Y. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01123-9 · Cited by 4,514
PLUMED 2: New feathers for an old bird
Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C., & Bussi, G. (2014) · Computer Physics Communications · doi:10.1016/j.cpc.2013.09.018 · Cited by 3,479
How fast-folding proteins fold
Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980
Self-citationAtomic-level characterization of the structural dynamics of proteins
Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., et al. (2010) · Science · doi:10.1126/science.1187409 · Cited by 1,923
Self-citation
Research works printed but not linked: 3
- K. J. Bowers E. Chow H. Xu R. O. Dror M. P. Eastwood B. A. Gregersen J. L. Klepeis I. Kolossvary M. A. Moraes F. D. Sacerdoti J. K. Salmon Y. Shan D. E. Shaw in Proceedings of the 2006 Association for Computing Machinery (ACM)/Institute of Electrical and Electronics Engineers (IEEE) Conference on Supercomputing (ACM New York 2006); http://doi.acm.org/10.1145/1188455.1188544. · DOI · Paper page
- 10.1261/rna.051102.115 · doi:10.1261/rna.051102.115
- S. Hanot M. Bonomi C. H. Greenberg A. Sali M. Nilges M. Vendruscolo R. Pellarin Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps. bioRxiv 113951 [Preprint]. 25 January 2018. https://doi.org/10.1101/113951 · doi:10.1101/113951
Cited by
Martini 3: A general purpose force field for coarse-grained molecular dynamics
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
Salo-Ahen, O. M. H., Alanko, I., Bhadane, R., Bonvin, A. M. J. J., Honorato, R. V., Hossain, S., Juffer, A. H., Kabedev, A., Lahtela-Kakkonen, M., Larsen, A. S., et al. (2020) · Processes · doi:10.3390/pr9010071 · Cited by 659
Extreme dynamics in a biomolecular condensate
Galvanetto, N., Ivanović, M. T., Chowdhury, A., Sottini, A., Nüesch, M. F., Nettels, D., Best, R. B., & Schuler, B. (2023) · Nature · doi:10.1038/s41586-023-06329-5 · Cited by 365
Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure
Emenecker, R. J., Griffith, D., & Holehouse, A. S. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.08.039 · Cited by 259
AlphaFold prediction of structural ensembles of disordered proteins
Brotzakis, Z. F., Zhang, S., Murtada, M. H., & Vendruscolo, M. (2025) · Nature Communications · doi:10.1038/s41467-025-56572-9 · Cited by 99
Metadata
- Authors
- Bottaro, S., & Lindorff-Larsen, K.
- Venue
- Science
- Published
- 2018-07-27
- Volume
- 361
- Issue
- 6400
- Pages
- 355-360
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2883596424
- Cited by
- 293
- References
- 79
- FWCI
- 8.40
- Type
- journal article
- Language
- en
- Open access
- closed
- Funders
- Velux Fonden
- Lundbeckfonden (BRAINSTRUC)
- Novo Nordisk Fonden (Hallas-Møller stipend)
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Biophysical experiments and biomolecular simulations: A perfect match? https://app.cochat.ai/papers/10.1126/science.aat4010
- The paper
- Bottaro, S., & Lindorff-Larsen, K. (2018). Biophysical experiments and biomolecular simulations: A perfect match? Science. https://doi.org/10.1126/science.aat4010
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.