The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Molecular dynamics and protein function
Open accessAbstract
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F 1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.
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Cites
Protein folding and misfolding
Dobson, C. M. (2003) · Nature · doi:10.1038/nature02261 · Cited by 4,791
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
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Cited by
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky300 · Cited by 1,086
Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00584 · Cited by 446
The future of molecular dynamics simulations in drug discovery
Borhani, D. W., & Shaw, D. E. (2012) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9517-y · Cited by 313
“…step, the forces on each atom—determined from the ‘‘force field,’’ a collection of physics-based parameters that represent both bonded and non-bonded (e.g., van der Waals) inter-atomic forces—are computed and the atomic position and velocity are updated according to Newton’s laws of motion [26].”
BackgroundThe inevitable journey to being
Russell, M. J., Nitschke, W., & Branscomb, E. (2013) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2012.0254 · Cited by 174
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
Hertig, S., Latorraca, N. R., & Dror, R. O. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004746 · Cited by 118
Biomolecular simulation and modelling: status, progress and prospects
van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90
Long-range energy transfer in proteins
Piazza, F., & Sanejouand, Y.-H. (2009) · Physical Biology · doi:10.1088/1478-3975/6/4/046014 · Cited by 58
Bucher, M., Niebling, S., Han, Y., Molodenskiy, D., Hassani Nia, F., Kreienkamp, H.-J., Svergun, D., Kim, E., Kostyukova, A. S., Kreutz, M. R., et al. (2021) · eLife · doi:10.7554/elife.66165 · Cited by 33
Bonati, L., Corrada, D., Giani Tagliabue, S., & Motta, S. (2017) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2017.01.011 · Cited by 27
Qin, H., Lim, L., & Song, J. (2012) · BMC Biophysics · doi:10.1186/2046-1682-5-2 · Cited by 23
Huan, X., Shi, J., Lim, L., Mitra, S., Zhu, W., Qin, H., Pasquale, E. B., & Song, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074040 · Cited by 16
AI-Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly
Zhang, W., Sun, C., Xu, Z., & Xu, W. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c01431 · Cited by 3
Elder, L. H., & Onufriev, A. V. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c02263 · Cited by 2
Metadata
- Authors
- Karplus, M., & Kuriyan, J.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-05-03
- Volume
- 102
- Issue
- 19
- Pages
- 6679-6685
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2058206198
- Cited by
- 1,144
- References
- 2
- FWCI
- 12.91
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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