The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Making it rain: cloud-based molecular simulations for everyone
Open accessPreprint — published as 10.1021/acs.jcim.1c00998 · Paper page
Abstract
We present a user-friendly front-end for running molecular dynamics (MD) simulations using OpenMM toolkit on the Google Colab framework. Our goals are: 1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and 2) to exemplify how low-income research groups can perform MD simulations in the microsecond timescale. We hope this work facilitates teaching and learning of molecular simulation throughout the community.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025
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Metadata
- Authors
- Arantes, P. R., Depólo Polêto, M., Pedebos, C., & Ligabue-Braun, R.
- Affiliations
- University of California, Riverside (US)
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- University of Southampton (GB)
- Department of Pharmacosciences, Federal University of Health Sciences of Proto ALegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
- Corresponding author
- Arantes, Pablo Ricardo
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-08-16
- Volume
- 61
- Issue
- 10
- Pages
- 4852-4856
- ISSN
- 1549-9596 (ISSN-L)
- OpenAlex
- W3203800312
- Cited by
- 148
- References
- 2
- Citations by year
- 2026: 47 · 2025: 30 · 2024: 27 · 2023: 30 · 2022: 14
- FWCI
- 10.74
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Topics
- Social Sciences › Education › Various Chemistry Research Topics
- Social Sciences › Education › Innovative Educational Technologies
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- molecular dynamics, OpenMM, Google Colab, cloud computing
- MeSH terms
- Cloud Computing, Molecular Dynamics Simulation
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