The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
Open accessAbstract
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
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
Phosphoinositides in cell regulation and membrane dynamics
Di Paolo, G., & De Camilli, P. (2006) · Nature · doi:10.1038/nature05185 · Cited by 2,790
Cited by
Wassenaar, T. A., Ingólfsson, H. I., Böckmann, R. A., Tieleman, D. P., & Marrink, S. J. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00209 · Cited by 1,174
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
Qi, Y., Ingólfsson, H. I., Cheng, X., Lee, J., Marrink, S. J., & Im, W. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00513 · Cited by 494
Self-citationHsu, P., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, S., & Im, W. (2017) · Journal of Computational Chemistry · doi:10.1002/jcc.24895 · Cited by 202
Self-citationZhao, F., Zhou, Q., Cong, Z., Hang, K., Zou, X., Zhang, C., Chen, Y., Dai, A., Liang, A., Ming, Q., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28683-0 · Cited by 149
Ins and outs of AlphaFold2 transmembrane protein structure predictions
Hegedűs, T., Geisler, M., Lukács, G. L., & Farkas, B. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04112-1 · Cited by 127
Metadata
- Authors
- Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., Qi, Y., Lee, J., Monje-Galvan, V., Venable, R. M., Klauda, J. B., & Im, W.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2014-08-07
- Volume
- 35
- Issue
- 27
- Pages
- 1997-2004
- ISSN
- 0192-8651 (ISSN-L)
- OpenAlex
- W1990771438
- Cited by
- 2,656
- References
- 3
- FWCI
- 29.20
- Type
- journal article
- Language
- en
- Open access
- green
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- Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., Qi, Y., Lee, J., Monje-Galvan, V., Venable, R. M., Klauda, J. B., & Im, W. (2014). CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. https://doi.org/10.1002/jcc.23702
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