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The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems
Open accessAbstract
Ab initio molecular dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing number of applications to biochemical systems. Here we describe the principles on which ab initio MD is based. We focus on the most popular implementation, based on density functional theory and plane wave basis set. By a survey of recent applications, we show that despite the current limitations of size and time scale, ab initio MD (and hybrid ab initio MD/MM approaches) can play an important role for the modeling of biological systems. Finally, we provide a perspective for the advancement of methodological approaches which may further expand the scope of ab initio MD in biomolecular modeling.
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Cites
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Trong, I. L., Teller, D. C., Okada, T., Stenkamp, R. E., et al. (2000) · Science · doi:10.1126/science.289.5480.739 · Cited by 5,637
Cited by
Proton Transfer 200 Years after von Grotthuss: Insights from Ab Initio Simulations
Marx, D. (2006) · ChemPhysChem · doi:10.1002/cphc.200600128 · Cited by 920
Ribas-Arino, J., & Marx, D. (2012) · Chemical Reviews · doi:10.1021/cr200399q · Cited by 448
Noodleman, L., Lovell, T., Han, W.-G., Li, J., & Himo, F. (2004) · Chemical Reviews · doi:10.1021/cr020625a · Cited by 373
Huggins, D. J., Biggin, P. C., Dämgen, M. A., Essex, J. W., Harris, S. A., Henchman, R. H., Khalid, S., Kuzmanic, A., Laughton, C. A., Michel, J., et al. (2019) · WIREs Computational Molecular Science · doi:10.1002/wcms.1393 · Cited by 169
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
Metadata
- Authors
- Carloni, P., Rothlisberger, U., & Parrinello, M.
- Venue
- Accounts of Chemical Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-05-15
- Volume
- 35
- Issue
- 6
- Pages
- 455-464
- ISSN
- 0001-4842 (ISSN-L)
- 1520-4898
- OpenAlex
- W2056661808
- Cited by
- 312
- References
- 1
- FWCI
- 11.42
- Type
- journal article
- Language
- en
- Open access
- green
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- Carloni, P., Rothlisberger, U., & Parrinello, M. (2002). The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems. Accounts of Chemical Research. https://doi.org/10.1021/ar010018u
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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.
