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Open Source Science

https://github.com/choderalab/aura-materials

Code and data for AurA simulations

https://github.com/choderalab/aura-materials

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 7 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.9%) to scientific vocabulary

Keywords

aurora aurora-kinase biophysics biorxiv chemical-biology computational-biology computational-chemistry elife kinase molecular-dynamics mskcc simulated-data simulation-data-analyzed structural-biology umn
Last synced: 5 months ago · JSON representation

Repository

Code and data for AurA simulations

Basic Info
  • Host: GitHub
  • Owner: choderalab
  • License: cc-by-4.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 279 MB
Statistics
  • Stars: 0
  • Watchers: 8
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Topics
aurora aurora-kinase biophysics biorxiv chemical-biology computational-biology computational-chemistry elife kinase molecular-dynamics mskcc simulated-data simulation-data-analyzed structural-biology umn
Created about 9 years ago · Last pushed almost 8 years ago

https://github.com/choderalab/AurA-materials/blob/master/ 

[![DOI](https://zenodo.org/badge/79592180.svg)](https://zenodo.org/badge/latestdoi/79592180)

# 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](http://dx.doi.org/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](https://doi.org/10.7554/eLife.32766) 


Complete Folding@home simulation data analyzed for the Cyphers publication is available via the [Open Science Framework](https://osf.io/afg8h/).
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](https://opensource.org/licenses/MIT) - 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](https://creativecommons.org/licenses/by/4.0/) - a copy of this license is provided as `DATA_LICENSE`

## Manifest

* `tpx2-paper/` - [jupyter](http://jupyter.org/) notebooks to analyze processed simulation data for the Cyphers paper 
* `phosphorylation-paper/` - all of the scripts and [jupyter](http://jupyter.org/) notebooks used to process the simulation data for the Ruff paper

Owner

  • Name: Chodera lab // Memorial Sloan Kettering Cancer Center
  • Login: choderalab
  • Kind: organization
  • Email: john.chodera@choderalab.org
  • Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY

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