Last modified by giuliadarrigo on 2023/06/26 14:11
From version 24.1
edited by dariak
on 2021/01/17 10:04
Change comment: There is no comment for this version
To version 44.1
edited by giuliadarrigo
on 2023/06/26 14:11
Change comment: There is no comment for this version

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Title
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1 -Molecular Tools: computation of unbinding rates
1 +Molecular Tools: computation of dissociation rates
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1 -XWiki.dariak
1 +XWiki.giuliadarrigo
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= Molecular Tools: computation of unbinding rates =
5 +(((
6 += Molecular Tools: computation of dissociation rates =
7 +)))
6 6  
7 -Authors:  D. Kokh
9 +This collab contains a set of tools and tutorials for analysing and computing unbinding rates of protein-small molecule and protein-protein complexes.
10 +
11 +Authors:  D. Kokh, G. D'Arrigo, R. Wade
8 8  )))
9 9  )))
10 10  
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14 14  (((
15 15  = What can I find here? =
16 16  
17 -* Jupyter Lab workflows that helps to setup, carry out, and analyze dissociation of protein-drug and protein-protein complexes
21 +Jupyter Lab workflows that help to set up, carry out and analyze dissociation of protein-drug and protein-protein complexes.
18 18  
23 +
24 +(% style="text-align:center" %)
25 +[[image:workflow.png||alt="tauRAMD_workflow"]]
26 +
27 +
19 19  = Who has access? =
20 20  
21 21  All EBRAINS users
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25 25  
26 26  (% class="box" %)
27 27  (((
28 -**Computation of Protein-Protein Unbinding rates**:  Jupyter Notebooks/PP-kinetics.ipynb
37 +**Computation of Protein-Ligand Dissociation rates**: 
29 29  
30 -[[https:~~/~~/lab.ebrains.eu/user/dariak/lab/tree/drive/Shared%20with%20all/Molecular%20Tools:%20computation%20of%20%20unbinding%20rates%20>>https://lab.ebrains.eu/user/dariak/lab/tree/drive/Shared%20with%20groups/Molecular%20Tools:%20computation%20of%20%20unbinding%20rates%20]]
39 +**1st_tutorial_tauRAMD_residencetime.ipynb** to estimate residence time from pre-computed RAMD trajectories.
31 31  
41 +**2nd_tutorial_tauRAMD_egress-routes.ipynb **to investigate dissociation pathways from pre-computed RAMD trajectories.
32 32  
33 -**Computation of Protein-Ligand Unbinding rates**:  under development
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
45 +{{/jupyterlink}}
46 +
47 +**Computation of Protein-Protein Dissociation rates**:
48 +
49 +under development
50 +
51 +{{jupyterlink}}
52 +https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Archive/PP-kinetics.ipynb
53 +{{/jupyterlink}}
34 34  )))
35 35  
36 36  
workflow.png
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