Last modified by richtesn on 2023/06/14 12:18
From version 9.1
edited by richtesn
on 2023/06/14 12:18
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To version 3.1
edited by richtesn
on 2021/06/11 14:54
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10 10  
11 11  == Background ==
12 12  
13 -~* For details on computation of the electrostatic potential see [[Calculate electrostatic potential>>doc:Collabs.computation-of-protein-association-rates.d.WebHome]].
13 +~* For details on computation of the electrostatic potential see :ref:`electrostatic_potential`.
14 14  
15 -~* For details on the similarity computations and [[pipsa algorithm>>doc:Collabs.computation-of-protein-association-rates.Compare a specific region of the electrostatic potentials surrounding a set of protein isoforms with multipipsa.WebHome]].
15 +~* For details on the similarity computations and pipsa algorithm, see :ref:`el_multipipsa`
16 16  
17 17  == Input Data ==
18 18  
19 -In this use case, we use as our input structure a structure of the catalytic domain of the enzyme adenylyl cyclase 5 (AC5), modelled during the work described in [[Tong et al. (2016)>>https://doi.org/10.1002/prot.25167]]
19 +In this use case, we use as our input structure a structure of the catalytic domain of the enzyme adenylyl cyclase 5 (AC5), modelled during the work described in |doi_tong|.
20 20  
21 21  The structures of the AC isoforms were created via homology modelling using the same template. The region where there are significant structural differences between the isoforms is in a flexible loop region that was not defined in the template structure. There are also variations in sequence length across AC isoforms in this region.
22 22  
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39 39  (% style="text-align:center" %)
40 40  [[image:Similarity.png||alt="Electrostatic Similarity" height="349" width="500"]]
41 41  
42 -== Related Jupyter Notebook ==
43 -
44 -Please note: In the lab where the notebook is running, please select the kernel: EBRAINS-23.02
45 -
46 -{{jupyterlink}}
47 -https://lab.ebrains.eu/user-redirect/lab/tree/shared/Molecular%20Tools:%20protein%20association%20rates%20and%20binding%20sites/JN/Identify_potential_protein_binding_sites_of_a_set_of_protein_isoforms.ipynb
48 -{{/jupyterlink}}
42 +