Warning:  Due to planned infrastructure maintenance, the EBRAINS Wiki and EBRAINS Support system will be unavailable for up to three days starting Monday, 14 July. During this period, both services will be inaccessible, and any emails sent to the support address will not be received.

Attention: We are currently experiencing some issues with the EBRAINS Drive. Please bear with us as we fix this issue. We apologise for any inconvenience caused.


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

 

Contents