The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
Open accessAbstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate (MTS) spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.
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Cites
Adding New Chemistries to the Genetic Code
Liu, C. C., & Schultz, P. G. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052308.105824 · Cited by 1,725
Activation pathway of Src kinase reveals intermediate states as targets for drug design
Shukla, D., Meng, Y., Roux, B., & Pande, V. S. (2014) · Nature Communications · doi:10.1038/ncomms4397 · Cited by 333
Self-citation
Cited by
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-citationCHARMM 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-citationQiu, D., Pei, J. V., Rosling, J. E. O., Thathy, V., Li, D., Xue, Y., Tanner, J. D., Penington, J. S., Aw, Y. T. V., Aw, J. Y. H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33403-9 · Cited by 70
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP
del Alamo, D., Govaerts, C., & Mchaourab, H. S. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26138 · Cited by 29
(2023) · doi:10.7554/elife.84645 · Cited by 22
Efficacy and mechanism of action of cipargamin as an antibabesial drug candidate
Li, H., Ji, S., Ariefta, N. R., Galon, E. M. S., El-Sayed, S. A., Do, T., Jia, L., Sakaguchi, M., Asada, M., Nishikawa, Y., et al. (2025) · eLife · doi:10.7554/elife.101128 · Cited by 1
Efficacy and mechanism of action of cipargamin as an antibabesial drug candidate
Li, H., Ji, S., Ariefta, N. R., Galon, E. M. S., El-Sayed, S. A., Do, T., Jia, L., Sakaguchi, M., Asada, M., Nishikawa, Y., et al. (2025) · eLife · doi:10.7554/elife.101128.4 · Cited by 1
Metadata
- Authors
- Jo, S., Cheng, X., Islam, S. M., Huang, L., Rui, H., Zhu, A., Lee, H. S., Qi, Y., Han, W., Vanommeslaeghe, K., MacKerell, A. D., Roux, B., & Im, W.
- Venue
- Advances in Protein Chemistry and Structural Biology
- Publisher
- Elsevier
- Published
- 2014
- Volume
- 96
- Pages
- 235-265
- ISSN
- 1876-1623 (ISSN-L)
- OpenAlex
- W2405075761
- Cited by
- 363
- References
- 2
- FWCI
- 7.61
- Type
- book chapter
- Language
- en
- Open access
- green
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