Markov State Model of B2 Adrenergic Receptor analyzed in "Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways."
Abstract/Contents
- Abstract
- Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.
Description
| Type of resource | software, multimedia |
|---|---|
| Date created | [ca. 2011 - 2013] |
Creators/Contributors
| Author | Kohlhoff, Kai |
|---|---|
| Author | Lawrenz, Morgan |
| Author | Shukla, Diwakar |
| Author | Bowman, Gregory |
| Author | Konerding, David |
| Author | Belov, Dan |
| Author | Altman, Russ |
| Author | Pande, Vijay |
Subjects
| Subject | molecular dynamics |
|---|---|
| Subject | cloud computing |
| Subject | G protein coupled receptors |
| Subject | computer-aided drug design |
| Genre | Dataset |
Bibliographic information
| Related Publication | K. J. Kohlhoff, D. Shukla, M. Lawrenz, G. R. Bowman, D. E. Konerding, D. Belov, R. B. Altman, V. S. Pande. (2014). Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry, 6, 15-21 (2014). http://dx.doi.org/10.1038/nchem.1821 |
|---|---|
| Location | https://purl.stanford.edu/vp873ky1987 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Share Alike 3.0 Unported license (CC BY-SA).
Preferred citation
- Preferred Citation
- Kohlhoff, Kai and Lawrenz, Morgan and Shukla, Diwakar and Bowman, Gregory and Konerding, David and Belov, Dan and Altman, Russ and Pande, Vijay. Markov State Model of B2 Adrenergic Receptor analyzed in "Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways." Stanford Digital Repository. Available at: http://purl.stanford.edu/vp873ky1987K.
Collection
Folding@home Collection
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- Contact
- mlawrenz@stanford.edu
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