Prediction of full-length all-atom structures of $\alpha_{IIb}\beta_{3}$ integrin along its minimum free energy activation pathway

This repository contains the data, codes, and analysis scripts for finding structures along a minimum free energy pathway connecting the inactive and active conformational states of $\alpha_{IIb}\beta_{3}$ integrin using finite temperature string method. For methodological details on the structures generated along the initial guess string, please refer to the follwing repo: https://github.com/Ferg-Lab/integrin_molgen.git.

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Overview

1. data: Relaxed structures from final iteration.
2. example_scripts: Simulation scripts.
3. notebooks: Analysis notebooks.

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Cite

If you use the codes or notebooks from this repo in your work, please cite:

S. Dasetty, R.C.Coffman, T. C. Bidone, and A. L. Ferguson. "Prediction of full-length all-atom structures of $\alpha_{IIb}\beta_{3}$ integrin along its minimum free energy activation pathway" Biophys J. (in preparation). DOI: XXXX

@article{ferglab2024Integrin,
  title={Prediction of full-length all-atom structures of $\alpha_{IIb}\beta_{3}$ integrin along its minimum free energy activation pathway,
  author={Dasetty, S. and Coffman, R.C. and Bidone, T.C. and Ferguson, A.L.},
  journal={XXXX},
  volume={XXXX},
  number={XXXX},
  pages={XXXX-XXXX},
  year={2023},
  publisher={XXXX}
}