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VGPReys
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VGPReys
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I am only half way.
Will continue later.
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Thank you for the detailed review! UPD: all commenets incorporated, ready for the second part:) |
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Covalently bound to one, and interact with another for the transfer to happen
… On 16 Mar 2026, at 23:26, Victor Reys ***@***.***> wrote:
Interact ?
or covalently bound ?
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We don’t distinguish anymore between expert and guru. So elevated is in principle the correct wording.
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@amjjbonvin litttle question. I found two saved server runs for the E2A-HPR system described in this tutorial. One result page linked inside the tutorial (https://wenmr.science.uu.nl/haddock2.4/result/4242424242/195967-E2A-HPR) and another one linked in “Example” tab of HADDOCK server (https://wenmr.science.uu.nl/haddock2.4/result/4242424242/0-E2A-HPR) Wonder if we need to keep both or if it’s fine to keep only one of these result pages permanently available? |
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If they are the same, then the second one is a simpler link
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VGPReys
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VGPReys
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VGPReys
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| **Note:** The same procedure can be used to introduce a mutation in an input protein structure. | ||
| To introduce this modification: | ||
| <a class="prompt prompt-info">Open the PDB file *e2a_1F3G.pdb* in your favorite text editor</a> |
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Do we want to specify editors not to use ?
Or typical editors to use
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I don't think so. Also I cannot think of an editor that can open pdb format by default, but at the same time can't maintain pdb spacing
VGPReys
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Apr 15, 2026
| **Note:** The same procedure can be used to introduce a mutation in an input protein structure. | ||
| To introduce this modification: | ||
| <a class="prompt prompt-info">Open the PDB file *e2a_1F3G.pdb* in your favorite text editor</a> | ||
| <a class="prompt prompt-info">Find histidine with residue sequence number equal to 90</a> |
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| <a class="prompt prompt-info">Find histidine with residue sequence number equal to 90</a> | |
| <a class="prompt prompt-info">Find the histidine with residue number 90</a> |
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To me "residue number" is also way more habitual, but I would keep "residue sequence number", as it is in documentation linked bellow in the text. I hope this way very unexperienced users won't get confused.
And experiences users gonna understand as is
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amjjbonvin
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Apr 15, 2026
| hide lines<br> | ||
| </a> | ||
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| Since this is an NMR structure it does not contain any water molecules and we don't need to remove them. |
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Why remove this? It is relevant since we do remove the water for the first molecule
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Be aware that there is a copy of this tutorial we use for teaching purposes in the 2nd year bachelor course. Might need to be updated too, but keeping the questions. Check https://www.bonvinlab.org/education/NMRMolmod/ |
VGPReys
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Apr 15, 2026
| #### HADDOCK submission: Input data | ||
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| For this we will make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server. | ||
| Locate "[Submit a new job](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"}" button. Note that you are now in "Input data" tab. |
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| Locate "[Submit a new job](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"}" button. Note that you are now in "Input data" tab. | |
| Locate and click on the "[Submit a new job](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"}" button. Note that you are now in "Input data" tab. |
VGPReys
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| * **Step1:** In the field "Job name", define a name for your docking run, e.g. *E2A-HPR*. | ||
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| * **Step2:** Select the number of molecules to dock, in this case the default *2*. | ||
| * **Step2:** In the field "Number of molecules", select the number of molecules to dock, in this case 2. |
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| * **Step2:** In the field "Number of molecules", select the number of molecules to dock, in this case 2. | |
| * **Step2:** In the field "Number of molecules", select the number of molecules to dock, in this case 2, which is the default value. |
VGPReys
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Apr 15, 2026
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| **Note:** Leave all other options to their default values. | ||
| Leave all other options to their default values. | ||
| **_Note_** that you can fold and unfold the "Molecule 1 - input" section by clicking on the ▼ icon. This works for any section and subsection of HADDOCK server. |
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| **_Note_** that you can fold and unfold the "Molecule 1 - input" section by clicking on the ▼ icon. This works for any section and subsection of HADDOCK server. | |
| **_Note_** that you can fold and unfold the "Molecule 1 - input" section by clicking on the ▼ icon. This works for any section and subsection on the HADDOCK2.4 server. |
VGPReys
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Apr 15, 2026
| ##### Definition of restraints | ||
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| #### Definition of restraints | ||
| In this tab, we will define distance restraints by specify active residues for each molecule. |
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| In this tab, we will define distance restraints by specify active residues for each molecule. | |
| In this tab, we will define distance restraints by specifying active residues for each molecule. |
VGPReys
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Apr 15, 2026
| The page will automatically refresh and the results will appear upon completions (which can take between 1/2 hour to several hours depending on the size of your system and the load of the server). You will be notified by email once your job has successfully completed. | ||
| This run will take between 30 minutes to several hours - depending on the load of the server. You will be notified by email once your job has been completed. The results will remain accessible for a week. | ||
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| You do not have to keep this page open, all resent jobs can be accessed via the "[Workspace](https://wenmr.science.uu.nl/haddock2.4/workspace){:target="_blank"}" button in the navigation bar. |
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| You do not have to keep this page open, all resent jobs can be accessed via the "[Workspace](https://wenmr.science.uu.nl/haddock2.4/workspace){:target="_blank"}" button in the navigation bar. | |
| You do not have to keep this page open, all recent jobs can be accessed via the "[Workspace](https://wenmr.science.uu.nl/haddock2.4/workspace){:target="_blank"}" button in the navigation bar. |
VGPReys
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Apr 15, 2026
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| Once your run has completed you will be presented with a result page showing the cluster statistics and some graphical representation of the data (and if registered, you will also be notified by email). Such an example output page can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} in case you don't want to wait for the results of your docking run. | ||
| Once your run has completed (you will also be notified by email about it) you will be presented with a result page showing the cluster statistics and graphical representation of the run. | ||
| An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your docking run. |
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| An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your docking run. | |
| An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your own docking run. |
VGPReys
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Apr 15, 2026
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| <a class="prompt prompt-question">Inspect the result page</a> | ||
| <a class="prompt prompt-question">How many clusters are generated?</a> | ||
| <a class="prompt prompt-question">Inspect the result page. How many clusters have been generated?</a> |
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At that stage, do we want to make a description of the different parts available on the page ?
VGPReys
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Apr 15, 2026
| HADDOCK_score = 1.0 * E_vdw + 0.2 * E_elec + 1.0 * E_desol + 0.1 * E_air, | ||
| </pre> | ||
| where Evdw is the intermolecular van der Waals energy, Eelec the intermolecular electrostatic energy, Edesol represents an empirical desolvation energy term adapted from Fernandez-Recio *et al.* J. Mol. Biol. 2004, and Eair the AIR energy. The cluster numbering reflects the size of the cluster, with cluster 1 being the most populated cluster. The various components of the HADDOCK score are also reported for each cluster on the results web page. | ||
| where *E_vdw* is the intermolecular van der Waals energy, *E_elec* is the intermolecular electrostatic energy, *E_desol* represents an empirical desolvation energy term adapted from Fernandez-Recio *et al.* J. Mol. Biol. 2004, and *E_air* is a penalty for violation of the restraints. |
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what about adding a link to the publication itself ?
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| where *E_vdw* is the intermolecular van der Waals energy, *E_elec* is the intermolecular electrostatic energy, *E_desol* represents an empirical desolvation energy term adapted from Fernandez-Recio *et al.* J. Mol. Biol. 2004, and *E_air* is a penalty for violation of the restraints. | |
| where *E_vdw* is the intermolecular van der Waals energy, *E_elec* is the intermolecular electrostatic energy, *E_desol* represents an empirical desolvation energy term adapted from (Fernandez-Recio *et al.* J. Mol. Biol. 2004)[https://www.sciencedirect.com/science/article/pii/S0022283603013755], and *E_air* is a penalty for violation of the restraints. |
VGPReys
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Apr 15, 2026
| ## Visualisation | ||
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| The new HADDOCK2.4 server integrates the NGL viewer which allows you to quickly visualize a specific structure. For that click on the "eye" icon next to a structure. | ||
| HADDOCK server integrates the NGL viewer which allows you to quickly visualize a specific structure among clustered. For that click on the "eye" icon next to a structure. |
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| HADDOCK server integrates the NGL viewer which allows you to quickly visualize a specific structure among clustered. For that click on the "eye" icon next to a structure. | |
| HADDOCK server integrates the NGL viewer which allows you to quickly visualize a specific structure among clustered ones. For that click on the "eye" icon next to a structure. |
VGPReys
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Apr 15, 2026
| <a class="prompt prompt-question">Based on this analysis, which cluster does satisfy best the biolocal information?</a> | ||
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| <a class="prompt prompt-question">Is this cluster also the best ranked one?</a> | ||
| <a class="prompt prompt-question">Based on this analysis, which cluster fits biological information the mos does satisfy best the biological information? Is this cluster also the best ranked one?</a> |
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| <a class="prompt prompt-question">Based on this analysis, which cluster fits biological information the mos does satisfy best the biological information? Is this cluster also the best ranked one?</a> | |
| <a class="prompt prompt-question">Based on this analysis, which cluster best satisfies the biological information?> | |
| <a class="prompt prompt-question">Is this cluster also the best ranked one?</a> |
VGPReys
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Apr 15, 2026
| <a class="prompt prompt-pymol"> | ||
| alter (chain B and 1GGR), resv -=300<br> | ||
| </a> | ||
| This shift is critical for the RMDS calculation described below! |
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| This shift is critical for the RMDS calculation described below! | |
| This shift is critical for appropriate residue mapping when performing the RMDS calculation described below! |
rvhonorato
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Apr 16, 2026
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| Once your run has completed you will be presented with a result page showing the cluster statistics and some graphical representation of the data (and if registered, you will also be notified by email). Such an example output page can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} in case you don't want to wait for the results of your docking run. | ||
| Once your run has completed (you will also be notified by email about it) you will be presented with a result page showing the cluster statistics and graphical representation of the run. | ||
| An example output page for E2A-HPR docking can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/195967-E2A-HPR){:target="_blank"} - just in case you don't want to wait for the results of your docking run. |
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Is this related to this? https://github.com/haddocking/csbportal/issues/1496
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Issue #772