The DOI matches its Crossref record; 281 of the 281 references it cites were found in a registry or an index.
Molecular Dynamics Simulations of Membrane Permeability
Open accessAbstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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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
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136
Self-citationPermeability of membranes in the liquid ordered and liquid disordered phases
Ghysels, A., Krämer, A., Venable, R. M., Teague, W. E., Lyman, E., Gawrisch, K., & Pastor, R. W. (2019) · Nature Communications · doi:10.1038/s41467-019-13432-7 · Cited by 136
Self-citationOverlay databank unlocks data-driven analyses of biomolecules for all
Kiirikki, A. M., Antila, H. S., Bort, L. S., Buslaev, P., Favela-Rosales, F., Ferreira, T. M., Fuchs, P. F. J., Garcia-Fandino, R., Gushchin, I., Kav, B., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45189-z · Cited by 34
Understanding molecular motion mechanism of phase change materials in mesoporous MCM-41
Li, A., Chen, X., Guo, T., Hai, G., Liu, P., Yu, H., & Xu, J. (2021) · Microporous and Mesoporous Materials · doi:10.1016/j.micromeso.2020.110741 · Cited by 13
Metadata
- Authors
- Venable, R. M., Krämer, A., & Pastor, R. W.
- Venue
- Chemical Reviews
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-02-12
- Volume
- 119
- Issue
- 9
- Pages
- 5954-5997
- ISSN
- 0009-2665 (ISSN-L)
- 1520-6890
- OpenAlex
- W2911593691
- Cited by
- 394
- References
- 281
- FWCI
- 2.76
- Type
- journal article
- Language
- en
- Open access
- green
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