The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
AmberTools
Open accessAbstract
High Resolution Image Download MS PowerPoint Slide AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
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Cites
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Self-citation
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A hybrid quantum computing pipeline for real world drug discovery
Li, W., Yin, Z., Li, X., Ma, D., Yi, S., Zhang, Z., Zou, C., Bu, K., Dai, M., Yue, J., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-67897-8 · Cited by 67
“Our simulation started with the intricate system preparation using Amber software suite 86 , especially packages including pdb4amber, antechamber, parmchk2, tleap, etc, defining the fundamental molecular and environmental parameters.”
MethodSelf-citationStructural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex
Diao, X., Shang, Q., Guo, M., Huang, Y., Zhang, M., Chen, X., Liang, Y., Sun, X., Zhou, F., Zhuang, J., et al. (2025) · Nature communications · doi:10.1038/s41467-025-56574-7 · Cited by 72
“For MM/GBSA calculations, molecular mechanics energies and the non-polar contribution to the solvation free energy were computed with gmx-MMPBSA 75 , which was used to convert Gromacs trajectories into AMBER format with ParmEd (https://github.com/ParmEd/ParmEd), and subsequently the mmpbsa.py 76 module of AmberTools w…”
Protein representations: Encoding biological information for machine learning in biocatalysis
Harding-Larsen, D., Funk, J., Madsen, N. G., Gharabli, H., Acevedo-Rocha, C. G., Mazurenko, S., & Welner, D. H. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108459 · Cited by 38
Long, T., Li, D., Vale, G., Jiang, Y., Schmiege, P., Yang, Z. J., McDonald, J. G., & Li, X. (2024) · Cell · doi:10.1016/j.cell.2024.08.004 · Cited by 31
Metadata
- Authors
- Case, D. A., Aktulga, H. M., Belfon, K., Cerutti, D. S., Cisneros, G. A., Cruzeiro, V. W. D., Forouzesh, N., Giese, T. J., Götz, A. W., Gohlke, H., Izadi, S., Kasavajhala, K., Kaymak, M. C., King, E., Kurtzman, T., Lee, T.-S., Li, P., Liu, J., Luchko, T., Luo, R., Manathunga, M., Machado, M. R., Nguyen, H. M., O’Hearn, K. A., Onufriev, A. V., Pan, F., Pantano, S., Qi, R., Rahnamoun, A., Risheh, A., Schott-Verdugo, S., Shajan, A., Swails, J., Wang, J., Wei, H., Wu, X., Wu, Y., Zhang, S., Zhao, S., Zhu, Q., Cheatham, T. E., Roe, D. R., Roitberg, A., Simmerling, C., York, D. M., Nagan, M. C., & Merz, K. M.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2023-10-08
- Volume
- 63
- Issue
- 20
- Pages
- 6183-6191
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W4387440676
- Cited by
- 2,089
- References
- 1
- FWCI
- 295.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- CoChat. (2026). Citation check: AmberTools. https://app.cochat.ai/papers/10.1021/acs.jcim.3c01153
- The paper
- Case, D. A., Aktulga, H. M., Belfon, K., Cerutti, D. S., Cisneros, G. A., Cruzeiro, V. W. D., Forouzesh, N., Giese, T. J., Götz, A. W., Gohlke, H., Izadi, S., Kasavajhala, K., Kaymak, M. C., King, E., Kurtzman, T., Lee, T.-S., Li, P., Liu, J., Luchko, T., . . . Merz, K. M. (2023). AmberTools. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.3c01153
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
