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Molecular Tools: computation of dissociation rates

Last modified by giuliadarrigo on 2023/06/26 14:11

Molecular Tools: computation of  dissociation rates

This collab contains a set of tools and tutorials for analysing and computing unbinding rates of protein-small molecule and protein-protein complexes.

Authors:  D. Kokh, G. D'Arrigo, R. Wade

What can I find here?

Jupyter Lab workflows that help to set up, carry out and analyze dissociation of protein-drug and protein-protein complexes.

tauRAMD_workflow

Who has access?

All EBRAINS users

Jupyter notebooks:

Computation of Protein-Ligand Dissociation rates:  

1st_tutorial_tauRAMD_residencetime.ipynb to estimate residence time from pre-computed RAMD trajectories.

2nd_tutorial_tauRAMD_egress-routes.ipynb to investigate dissociation pathways from pre-computed RAMD trajectories.

https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Training_220623/Jupyter_Notebooks

Computation of Protein-Protein Dissociation rates: 

under development

https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Archive/PP-kinetics.ipynb

 

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