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rvhonorato merged 1 commit into from
Jun 30, 2026
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update links to wenmr.science.uu.nl #784

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6 changes: 3 additions & 3 deletions education/HADDOCK24/HADDOCK24-protein-glycan/index.md
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Expand Up @@ -313,7 +313,7 @@ Currently your run should be queued but eventually its status will change to "Ru

The page will automatically refresh and the results will appear upon completion of the run (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.

If you do not wish to wait for the run to finish, you can find the results of the run [at this link](https://rascar.science.uu.nl/haddock2.4/result/4242424242/488462-2zex-modeling).
If you do not wish to wait for the run to finish, you can find the results of the run [at this link](https://wenmr.science.uu.nl/haddock2.4/result/4242424242/488462-2zex-modeling).

<hr>
<hr>
Expand All @@ -326,7 +326,7 @@ If you do not wish to wait for the run to finish, you can find the results of th

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).

In case you do not want to wait for your runs to be finished, a precalculated run can be found [here](https://rascar.science.uu.nl/haddock2.4/result/4242424242/488462-2zex-modeling).
In case you do not want to wait for your runs to be finished, a precalculated run can be found [here](https://wenmr.science.uu.nl/haddock2.4/result/4242424242/488462-2zex-modeling).

<a class="prompt prompt-question">Inspect the result page</a>

Expand Down Expand Up @@ -525,7 +525,7 @@ The first line is a comment. The second and third lines contain the information

* **Step 5:** Click on the **Submit** button at the bottom left of the interface.

You can inspect the results of a precalculated run [here](https://rascar.science.uu.nl/haddock2.4/result/4242424242/488508-2zex-modeling-bonus).
You can inspect the results of a precalculated run [here](https://wenmr.science.uu.nl/haddock2.4/result/4242424242/488508-2zex-modeling-bonus).

<a class="prompt prompt-question">How many clusters are generated? Is the first cluster unambiguously better than the second and third ones? Are the HADDOCK scores better than in the previous case?</a>

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6 changes: 3 additions & 3 deletions education/HADDOCK24/LightDock-membrane-proteins/index.md
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Expand Up @@ -15,7 +15,7 @@ This tutorial consists of the following sections:

## Introduction

This tutorial demonstrates the use of [LightDock](https://lightdock.org){:target="_blank"} for predicting the structure of membrane receptor–soluble protein complex using the topological information provided by the membrane to guide the modeling process. The resulting LightDock models are then refined using [HADDOCK2.4 webserver](https://haddock.science.uu.nl/haddock2.4/). We will be following the protocol described in [Roel-Touris *et al*, 2020](https://www.nature.com/articles/s41467-020-20076-5){:target="_blank"}.
This tutorial demonstrates the use of [LightDock](https://lightdock.org){:target="_blank"} for predicting the structure of membrane receptor–soluble protein complex using the topological information provided by the membrane to guide the modeling process. The resulting LightDock models are then refined using [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4/). We will be following the protocol described in [Roel-Touris *et al*, 2020](https://www.nature.com/articles/s41467-020-20076-5){:target="_blank"}.

Membrane proteins are among the most challenging systems to study with experimental structural biology techniques, thus computational techniques such as docking might offer invaluable insights on the modeling of those systems.

Expand All @@ -30,7 +30,7 @@ In this tutorial we will be working with the crystal structure of _Mus musculus

<hr>

For this tutorial we will make use of the [HADDOCK2.4 webserver](https://haddock.science.uu.nl/haddock2.4){:target="_blank"} and [LightDock software](https://lightdock.org/){:target="_blank"}.
For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"} and [LightDock software](https://lightdock.org/){:target="_blank"}.

{% include paper_citation.html key="haddock24" %}

Expand Down Expand Up @@ -74,7 +74,7 @@ For more information about LightDock, please visit the [tutorials section](https

In order to run this tutorial you will need to have the following software installed: [LightDock][link-lightdock], [pdb-tools][link-pdbtools] and [PyMOL][link-pymol].

Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://haddock.science.uu.nl/auth/register/haddock](https://haddock.science.uu.nl/auth/register/haddock){:target="_blank"}.
Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock){:target="_blank"}.


### Installing LightDock
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2 changes: 1 addition & 1 deletion education/HADDOCK3/HADDOCK3-protein-glycan/index.md
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Expand Up @@ -146,7 +146,7 @@ When done, press Download Minimized Structure and download the PDB file.</a>
Unfortunately, the glycan structure we just obtained cannot be directly used in HADDOCK as the formant and the residue
and atom naming differ from the conventions used in HADDOCK (which follow the naming in the PDB).
We will need to edit it to remove the several TER statements GLYCAM placed between the monosaccharides,
and to add the [HADDOCK residue name](https://rascar.science.uu.nl/haddock2.4/library){:target="_blank"}
and to add the [HADDOCK residue name](https://wenmr.science.uu.nl/haddock2.4/library){:target="_blank"}
proper to beta-D-glucopyranose. Importantly, we have to merge the OH aglycon with the first monosaccharide unit,
as they are now separated in two different residues.

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4 changes: 2 additions & 2 deletions education/HADDOCK3/HADDOCK3-protein-peptide/index.md
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Expand Up @@ -232,12 +232,12 @@ These can be combined with logical operators AND, OR to construct more complex d
Please refer for that to the [online CNS manual](http://cns-online.org/v1.3/){:target="_blank"} for more info.


AIRs file (`.tbl`) can be generated using the `haddock3-restraints` command line tool (installed with haddock3) or a version [web version](https://rascar.science.uu.nl/haddock-restraints){:target="_blank"}.
AIRs file (`.tbl`) can be generated using the `haddock3-restraints` command line tool (installed with haddock3) or a version [web version](https://wenmr.science.uu.nl/haddock-restraints){:target="_blank"}.
We will explain how to use this tool shortly, but first we need to identify which residues participate in the interaction - both active and passive.

### Defining active residues for protein

[ARCTIC-3D](https://rascar.science.uu.nl/arctic3d/){:target="_blank"} is a data-mining tool that clusters all known interfaces of a protein, grouping similar interaction sites into residue sets that are likely to participate in binding.
[ARCTIC-3D](https://wenmr.science.uu.nl/arctic3d/){:target="_blank"} is a data-mining tool that clusters all known interfaces of a protein, grouping similar interaction sites into residue sets that are likely to participate in binding.
For mouse MDM2, no structural information is currently available, however, such data exists for its human homolog.
To define plausible active residues in mouse MDM2, we applied ARCTIC-3D to the human protein and transferred the results onto mouse variant.
Resulting residues were filtered based on their solvent accessibility:
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