Last modified by giuliadarrigo on 2023/06/26 14:11
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giuliadarrigo 37.1 6 = Molecular Tools: computation of dissociation rates =
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giuliadarrigo 33.1 9 This collab contains a set of tools and tutorials for analysing and computing unbinding rates of protein-small molecule and protein-protein complexes.
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11 Authors:  D. Kokh, G. D'Arrigo, R. Wade
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19 = What can I find here? =
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giuliadarrigo 34.1 21 Jupyter Lab workflows that help to set up, carry out and analyze dissociation of protein-drug and protein-protein complexes.
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25 [[image:workflow.png||alt="tauRAMD_workflow"]]
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dariak 1.1 28 = Who has access? =
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dariak 11.1 30 All EBRAINS users
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dariak 22.1 33 (% class="text-uppercase" %)Jupyter notebooks:
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giuliadarrigo 38.1 37 **Computation of Protein-Ligand Dissociation rates**: 
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giuliadarrigo 44.1 39 **1st_tutorial_tauRAMD_residencetime.ipynb** to estimate residence time from pre-computed RAMD trajectories.
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41 **2nd_tutorial_tauRAMD_egress-routes.ipynb **to investigate dissociation pathways from pre-computed RAMD trajectories.
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giuliadarrigo 42.1 43 {{jupyterlink}}
44 https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Training_220623/Jupyter_Notebooks
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giuliadarrigo 44.1 47 **Computation of Protein-Protein Dissociation rates**:
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giuliadarrigo 44.1 49 under development
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giuliadarrigo 43.1 51 {{jupyterlink}}
giuliadarrigo 44.1 52 https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Archive/PP-kinetics.ipynb
giuliadarrigo 43.1 53 {{/jupyterlink}}
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63 {{box title="**Contents**"}}
64 {{toc/}}
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