The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
Abstract
For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of one-particle-per-residue, CafeMol equips four structure-based protein models: (1) the off-lattice Go model, (2) the atomic interaction based CG model for native state and folding dynamics, (3) the multiple-basin model for conformational change dynamics, and (4) the elastic network model for quasiharmonic fluctuations around the native structure. Ligands can be treated either explicitly or implicitly. For mimicking functional motions of proteins driven by some external force, CafeMol has various and flexible means to "switch" the energy functions that induce active motions of the proteins. CafeMol can do parallel computation with modest sized PC clusters. We describe CafeMol methods and illustrate it with several examples, such as rotary motions of F1-ATPase and drug exports from a transporter. The CafeMol source code is available at www.cafemol.org .
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Cites
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Self-citationInternal strain regulates the nucleotide binding site of the kinesin leading head
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Determining structures of RNA conformers using AFM and deep neural networks
Degenhardt, M. F. S., Degenhardt, H. F., Bhandari, Y. R., Lee, Y.-T., Ding, J., Yu, P., Heinz, W. F., Stagno, J. R., Schwieters, C. D., Watts, N. R., et al. (2025) · Nature · doi:10.1038/s41586-024-07559-x · Cited by 56
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Terakawa, T., Higo, J., & Takada, S. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.06.026 · Cited by 32
Self-citationChromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure
(2025) · doi:10.1038/s41467-025-56197-y · Cited by 10
The molecular basis for hydrodynamic properties of PEGylated human serum albumin
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Baweja, L., & Wereszczynski, J. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00635-0 · Cited by 3
Gu, C., Takada, S., Brandani, G. B., & Terakawa, T. (2025) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012493 · Cited by 1
Self-citationYamauchi, M., Brandani, G. B., Terakawa, T., & Takada, S. (2026) · eLife · doi:10.7554/elife.106752
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Metadata
- Authors
- Kenzaki, H., Koga, N., Hori, N., Kanada, R., Li, W., Okazaki, K.-I., Yao, X.-Q., & Takada, S.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-05-19
- Volume
- 7
- Issue
- 6
- Pages
- 1979-1989
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2010713749
- Cited by
- 238
- References
- 9
- FWCI
- 3.17
- Type
- journal article
- Language
- en
- Open access
- closed
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