Repository containing the files regarding the study:

Exploring TAS2R46 Biomechanics through Molecular Dynamics and Network Analysis

Marco Cannariato¹, Riccardo Fanunza¹, Eric A. Zizzi¹, Marcello Miceli¹, Giacomo Di Benedetto², Marco A. Deriu¹ and Lorenzo Pallante^1*

¹Polito^BIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129, Turin, Italy
²7HC S.r.l., 00198, Rome, Italy

The preprint of the article can be accessed at this link

---

Repo Structure

The repository is organized in the following folders:

• MDP/

This folder contains the MD simulation parameters in GROMACS MDP format used for minimization, stepwise equilibration and production MD simulation.

• Topologies/

This folder contains the molecular topologies for the of Holo, Trans, and Apo states (as obtained from CHARMM-GUI).

• SimulationInput/

This folder contains the input files for the production of MD simulations (after NVT+NPT equilibration; one tpr per replica).

• Notebooks/

1. Conformational_analysis.ipynb
   Notebook containing the python codes used to perform the conformational analysis of TAS2R46
2. DYNET_analysis.ipynb
   Notebook containing the python codes used to perform the dynamic network analysis of TAS2R46

---

Acknowledgements:

The present work has been developed as part of the VIRTUOUS project, funded by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie-RISE Grant Agreement No. 872181 (https://www.virtuoush2020.com/).

This work has been conducted as part of the GALATEA project, which is funded by the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Actions (HORIZON-MSCA-2023-SE-01-01, Grant Agreement No. 101183057).