choderalab/aura-materials

Code and data for AurA simulations

AurA Folding@home simulations

This site archives explicit solvent trajectory data, scripts, and figures for the following publications:

Soreen Cyphers, Emily F Ruff, Julie M Behr, John D Chodera, and Nicholas M Levinson.
A water-mediated allosteric network governs activation of Aurora kinase A.
DOI: 10.1038/nchembio.2296

Emily F. Ruff, Joseph M. Muretta, Andrew Thompson, Eric Lake, Soreen Cyphers, Steven K. Albanese, Sonya M. Hanson, Julie M. Behr, David D. Thomas, John D. Chodera, Nicholas M. Levinson A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation DOI: 10.7554/eLife.32766

Complete Folding@home simulation data analyzed for the Cyphers publication is available via the Open Science Framework. Complete Folding@home simulation data analyzed for the Ruff publication will be made available soon!

License

• The software in this repository is made available under the MIT License - a copy of this license is provided as SOFTWARE_LICENSE
• The data in this repository is made available under the CC BY 4.0 License - a copy of this license is provided as DATA_LICENSE

Manifest

• tpx2-paper/ - jupyter notebooks to analyze processed simulation data for the Cyphers paper
• phosphorylation-paper/ - all of the scripts and jupyter notebooks used to process the simulation data for the Ruff paper

aura-materials's Issues

Add bioRxiv link for second paper

We should link to the DOI for the bioRxiv submission for the second paper:

https://doi.org/10.1101/205260

License

Following the guidance of this Victoria Stodden paper, we should add licenses for the coda and data made available in this repo:

• All code should be made available under the permissive OSI-approved MIT License
• All data should be made available under the CC BY 4.0 License - legal code

@steven-albanese : Could you add the formatted text versions of this to the repo and update the README.md to reflect these licenses?

Upload F@H data to OSF

I'm not sure where @jchodera is in the process here. The README with project and RUN numbers used for the phosphorylation paper are here: https://github.com/choderalab/AurA-materials/tree/master/phosphorylation-paper

Rename directories?

The terms "first paper" and "second paper" don't make much sense here. Perhaps we could rename the directories to match DOIs, or citations, or even just short keywords (like tpx2-paper and phosphorylation-paper)?