A collection of Google Colab notebooks for setting up protein-membrane systems.
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Based on the notebooks from pstansfeld/MemProtMD
References
- Nugent & Jones (2013) Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-14-276 [https://github.com/psipred/MemEmbed]
- Souza et al. (2021) Martini 3: a general-purpose force field for coarse-grained molecular dynamics. Nature Methods. https://doi.org/10.1038/s41592-021-01098-3 [https://github.com/marrink-lab/vermouth-martinize]
- Wassenaar et al. (2015) Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. JCTC. https://doi.org/10.1021/acs.jctc.5b00209 [https://github.com/Tsjerk/Insane]
- Stansfeld et al. (2015) MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes. Structure. https://doi.org/10.1016/j.str.2015.05.006
- Abraham et al. (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputer. SoftwareX. https://doi.org/10.1016/j.softx.2015.06.001
- Vickery & Stansfeld (2021) CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations. JCTC. https://doi.org/10.1021/acs.jctc.1c00295 [https://github.com/pstansfeld/cg2at]
- Jurrus et al. (2018) Improvements to the APBS biomolecular solvation software suite. Protein Science. https://onlinelibrary.wiley.com/doi/10.1002/pro.3280