{
@@ -683,7 +683,7 @@ to allow the runs to complete within a reasonable amount of time. Because of tha
We have already performed a full docking runs (with 2000/400/400 models generated for the
rigid-body docking, semi-flexible and final refinement stages).
-The full run can be accessed [here](https://bianca.science.uu.nl/haddock2.4/run/4242424242/PolIII-C82-C34-C31model-xlinks){:target="_blank"}.
+The full run can be accessed [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/PolIII-C82-C34-C31model-xlinks){:target="_blank"}.
@@ -1252,7 +1252,7 @@ Can you identify possible problematic areas of the interface?
To refine the fitted models, we can use HADDOCK, keeping the molecules in their original orientation, skipping the initial rigid body docking stage and semi-flexible refimenent and only performing the final refinement (or morphing from CG to AA if coarse graining is used). Since we are dealing with severe clashes, a coarse graining approach would be better since the individual all atom representation are effectively docked onto the coarse-grained model and refined.
-We will make use of the [HADDOCK2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
+We will make use of the [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
* **Step 1:** Define a name for your refinement run, e.g. *PolIII-core-C82-refine*.
@@ -1359,7 +1359,7 @@ Number of MD steps during third cooling stage with fully flexible interface -> 0
We are now ready to submit the docking run.
-If you don't want to wait for your results, a pre-calculated refinement run is available [here](https://bianca.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-refine){:target="_blank"}.
+If you don't want to wait for your results, a pre-calculated refinement run is available [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-refine){:target="_blank"}.
Inspect the results page: Are the intermolecular energies favorable?
@@ -1385,7 +1385,7 @@ We will now repeat the steps from the the first [HADDOCK run submission](#strate
with as difference that we will use the PowerFit/Chimera, HADDOCK-refined structures of PolIII core and C82. Those will be kept fixed in their original positions
for the initial rigid-body docking stage.
-Connect to the [HADDOCK2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
+Connect to the [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
* **Step 1:** Define a name for your docking run, e.g. *PolIII-core-C82-EMfit-C34-C31-xlinks*.
@@ -1510,7 +1510,7 @@ We are now ready to submit the docking run!
### Analysis of the docking results
-Once your run has completed you will be presented with the result page. You can also access a pre-calculated run following the docking scenario just described from the following [link](https://bianca.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-EMfit-C34-C31-xlinks){:target="_blank"}.
+Once your run has completed you will be presented with the result page. You can also access a pre-calculated run following the docking scenario just described from the following [link](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-EMfit-C34-C31-xlinks){:target="_blank"}.
Inspect the results page
@@ -1594,10 +1594,10 @@ In that case you should setup a six-body docking run using:
and as restraint files: `xlinks-all-inter-disvis-filtered-C31dummyLYS.tbl` for the cross-links and `C31-C34-connectivities.tbl` as connectivity restraints.
The results of such a run using exclusively cross-links (strategy 1) can be accessed
-[here](https://bianca.science.uu.nl/haddock2.4/run/4242424242/RNA-Pol-III-xlinks-C31dummies){:target="_blank"}.
+[here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/RNA-Pol-III-xlinks-C31dummies){:target="_blank"}.
The results of such a run using the cryo-EM fitted core and C82 domains with cross-links (strategy 2) can be accessed
-[here](https://bianca.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-EMfit-C34-C31dummies){:target="_blank"}.
+[here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/PolIII-core-C82-EMfit-C34-C31dummies){:target="_blank"}.
2) Try to identify from the run described in this tutorial the heavily violated cross-links and remove them from the restraints list.
Repeat the docking and check if this affects the position of the various domains.
@@ -1613,19 +1613,19 @@ our [HADDOCK forum](https://ask.bioexcel.eu/c/haddock){:target="_blank"} hosted
[link-cns]: https://cns-online.org "CNS online"
[link-chimera]: https://www.cgl.ucsf.edu/chimera/ "UCSF Chimera"
[link-disvis]: https://github.com/haddocking/disvis "DisVis GitHub repository"
-[link-disvis-web]: hhttps://bianca.science.uu.nl/disvis "DisVis web server"
-[link-disvis-submit]: https://bianca.science.uu.nl/disvis/submit "DisVis submission"
-[link-disvis-register]: https://bianca.science.uu.nl/auth/register "DisVis registration"
+[link-disvis-web]: hhttps://wenmr.science.uu.nl/disvis "DisVis web server"
+[link-disvis-submit]: https://wenmr.science.uu.nl/disvis/submit "DisVis submission"
+[link-disvis-register]: https://wenmr.science.uu.nl/auth/register "DisVis registration"
[link-pymol]: https://www.pymol.org/ "PyMOL"
[link-haddock]: https://bonvinlab.org/software/haddock2.2 "HADDOCK 2.2"
[link-haddock-web]: https://wenmr.science.uu.nl/haddock2.4/ "HADDOCK 2.4 webserver"
[link-haddock-easy]: https://alcazar.science.uu.nl/services/HADDOCK2.2/haddockserver-easy.html "HADDOCK2.2 webserver easy interface"
[link-haddock-expert]: https://alcazar.science.uu.nl/services/HADDOCK2.2/haddockserver-expert.html "HADDOCK2.2 webserver expert interface"
-[link-haddock-register]: https://bianca.science.uu.nl/auth/register/"HADDOCK web server registration"
+[link-haddock-register]: https://wenmr.science.uu.nl/auth/register/"HADDOCK web server registration"
[link-molprobity]: http://molprobity.biochem.duke.edu "MolProbity"
[link-powerfit]: https://github.com/haddocking/powerfit "PowerFit"
[link-powerfit-web]: https://alcazar.science.uu.nl/services/POWERFIT/ "PowerFit web server"
-[link-powerfit-register]: https://bianca.science.uu.nl/auth/register "PowerFit registration"
+[link-powerfit-register]: https://wenmr.science.uu.nl/auth/register "PowerFit registration"
[link-powerfit-submit]: https://alcazar.science.uu.nl/cgi/services/POWERFIT/powerfit/submit "PowerFit submission"
[link-powerfit-help]: https://alcazar.science.uu.nl/cgi/services/POWERFIT/powerfit/help "PowerFit submission"
[link-xwalk]: https://www.xwalk.org
diff --git a/education/HADDOCK24/XL-MS-oligomer/index.md b/education/HADDOCK24/XL-MS-oligomer/index.md
index d7141c23..3bfea552 100644
--- a/education/HADDOCK24/XL-MS-oligomer/index.md
+++ b/education/HADDOCK24/XL-MS-oligomer/index.md
@@ -184,7 +184,7 @@ A 132 CA B 161 CA 3.0 10.0
We have all input data required to run DisVis. To launch the run go to:
-https://bianca.science.uu.nl/disvis
+https://wenmr.science.uu.nl/disvis
On this page, you will find the most relevant information about the server.
@@ -231,7 +231,7 @@ Once your job has completed, and provided you did not close the status page, you
page (you will also receive an email notification).
If you don't' want to wait for your run to complete, you can access the precalculated results of a run submitted
-with the same input and complete scanning [here](https://bianca.science.uu.nl/disvis/run/gQH_3T7grzrD){:target="_blank"}.
+with the same input and complete scanning [here](https://wenmr.science.uu.nl/disvis/run/gQH_3T7grzrD){:target="_blank"}.
The results page presents a summary split into several sections:
@@ -353,7 +353,7 @@ Let's now setup the docking run!
#### Registration / Login
-In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://bianca.science.uu.nl/auth/register/){:target="_blank"}. To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
+In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://wenmr.science.uu.nl/auth/register/){:target="_blank"}. To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
**Note:** The blue bars on the server can be folded/unfolded by clicking on the arrow on the left
@@ -681,9 +681,9 @@ If you download the results, you can visualize the prediction confidence in PyMo
[link-cns]: https://cns-online.org "CNS online"
[link-disvis]: https://github.com/haddocking/disvis "DisVis GitHub repository"
-[link-disvis-web]: https://bianca.science.uu.nl/disvis "DisVis web server"
-[link-disvis-submit]: https://bianca.science.uu.nl/disvis/submit "DisVis submission"
-[link-disvis-register]: https://bianca.science.uu.nl/auth/register "DisVis registration"
+[link-disvis-web]: https://wenmr.science.uu.nl/disvis "DisVis web server"
+[link-disvis-submit]: https://wenmr.science.uu.nl/disvis/submit "DisVis submission"
+[link-disvis-register]: https://wenmr.science.uu.nl/auth/register "DisVis registration"
[link-data]: https://www.bonvinlab.org/education/HADDOCK24/XL-MS-oligomer/XL-MS-oligomer.zip "DisVis tutorial data"
[link-chimera]: https://www.cgl.ucsf.edu/chimera/ "UCSF Chimera"
[link-chimera-distance]: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html "UCSF Chimera distance command"
@@ -693,5 +693,5 @@ If you download the results, you can visualize the prediction confidence in PyMo
[link-haddock]: https://bonvinlab.org/software/haddock2.4 "HADDOCK2.4"
[link-haddock-web]: https://wenmr.science.uu.nl/haddock2.4/ "HADDOCK2.4 webserver"
[link-haddock-multi]: https://wenmr.science.uu.nl/haddock2.4/submit/1 "HADDOCK2.4 docking interface"
-[link-haddock-register]: https://bianca.science.uu.nl/auth/register/ "HADDOCK2.4 registration"
+[link-haddock-register]: https://wenmr.science.uu.nl/auth/register/ "HADDOCK2.4 registration"
[link-haddock-tutorial]: https://bonvinlab.org/education/HADDOCK24/HADDOCK24-protein-protein-basic "HADDOCK2.4 webserver tutorial"
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2024/index.md b/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2024/index.md
index fd4a9b3c..5d385c68 100644
--- a/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2024/index.md
+++ b/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2024/index.md
@@ -578,7 +578,7 @@ Here, since we are using a local version, we need to define those manually.
This can easily be done using a haddock3 command line tool in the following way:
-haddock3-restraints passive_from_active 4I1B_clean.pdb 72,73,74,75,81,83,84,89,90,92,94,96,97,98,115,116,117 --cutoff 0.15
+haddock3-restraints passive_from_active 4I1B_clean.pdb 72,73,74,75,81,83,84,89,90,92,94,96,97,98,115,116,117 \-\-cutoff 0.15
The command prints a list of passive residues, which you should save to a file for further use.
diff --git a/education/NMRMolmod/index.md b/education/NMRMolmod/index.md
index af47d42d..b62e877e 100644
--- a/education/NMRMolmod/index.md
+++ b/education/NMRMolmod/index.md
@@ -17,7 +17,7 @@ This computer practical consists of the following sections:
This practical will demonstrate the use of HADDOCK for predicting the structure of a protein-protein complex from NMR chemical shift perturbation (CSP) data. Namely, you will dock two E. coli proteins involved in glucose transport: the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr). The structures in the free form have been determined using X-ray crystallography (E2A) (PDB ID [1F3G](https://www.ebi.ac.uk/pdbe/entry/pdb/1f3g)) and NMR spectroscopy (HPr) (PDB ID [1HDN](https://www.ebi.ac.uk/pdbe/entry/pdb/1hdn)). The structure of the native complex has also been determined with NMR (PDB ID [1GGR](https://www.ebi.ac.uk/pdbe/entry/pdb/1ggr)). These NMR experiments have also provided us with an array of data on the interaction itself. For this tutorial, you will only make use of interface residues identified from NMR chemical shift perturbation data as described in [Wang *et al*, EMBO J (2000)](http://onlinelibrary.wiley.com/doi/10.1093/emboj/19.21.5635/abstract).
-For this tutorial you will make use of the [HADDOCK2.4 webserver](https://bianca.science.uu.nl/haddock2.4).
+For this tutorial you will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4).
A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2/) can be found in the following publications:
@@ -43,7 +43,7 @@ You are expected to submit a report providing answers to all questions throughou
In order to run this practical you will need to have the following software installed: [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://bianca.science.uu.nl/auth/register/haddock](https://bianca.science.uu.nl/auth/register/haddock).
+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).
## HADDOCK general concepts
@@ -242,13 +242,13 @@ In order to use a modified amino-acid in HADDOCK, the only thing you will need t
#### Registration / Login
-In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://bianca.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
+In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://wenmr.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
**Note:** The blue bars on the server can be folded/unfolded by clicking on the arrow on the left
#### Submission and validation of structures
-For this we will make us of the [HADDOCK 2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1) of the HADDOCK web server.
+For this we will make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) of the HADDOCK web server.
In this stage of the submission process we can upload the structures we previously prepared with PyMOL.
@@ -306,7 +306,7 @@ Active residues (directly involved in the interaction) -> 15,16,17,20,48,49,51,5
#### Job submission
-This interface allows us to modify many parameters that control the behaviour of HADDOCK but in our case the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a haddockparameter file which contains all the settings and input structures for our run (in json format). We stronly recommend to download this file as it will allow you to repeat the run after uploading into the [file upload interface](https://bianca.science.uu.nl/haddock2.4/submit_file) of the HADDOCK webserver. It can serve as input reference for the run. This file can also be edited to change a few parameters for example.
+This interface allows us to modify many parameters that control the behaviour of HADDOCK but in our case the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a haddockparameter file which contains all the settings and input structures for our run (in json format). We stronly recommend to download this file as it will allow you to repeat the run after uploading into the [file upload interface](https://wenmr.science.uu.nl/haddock2.4/submit_file) of the HADDOCK webserver. It can serve as input reference for the run. This file can also be edited to change a few parameters for example.
* **Step 8:** Click on the "Submit" button at the bottom left of the interface.
diff --git a/education/biomolecular-simulations-2018/HADDOCK_tutorial/index.md b/education/biomolecular-simulations-2018/HADDOCK_tutorial/index.md
index bb4ead58..2872170d 100644
--- a/education/biomolecular-simulations-2018/HADDOCK_tutorial/index.md
+++ b/education/biomolecular-simulations-2018/HADDOCK_tutorial/index.md
@@ -37,7 +37,7 @@ instructions and/or PyMOL commands.
In order to run this tutorial you will need to have the following software installed: [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 our [registration page](https://bianca.science.uu.nl/auth/register/){: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 our [registration page](https://wenmr.science.uu.nl/auth/register/){:target="_blank"}.
> If you have questions, feedbacks or recommendations, either during the course of after, please post them on the dedicated topic we created on our [interest group forum](https://ask.bioexcel.eu/t/bioexcel-summer-school-2018-modelling-of-a-covalent-inhibitor-using-haddock-and-cpmd/){:target="_blank"}
@@ -292,7 +292,7 @@ or download it from [here](./media/unambig.tbl){:target="_blank"} for convenienc
## Submit your docking run
-**Note** *that fine-tuning the parameters of the web server to covalently dock a ligand requires the most advanced privilege on the web server. If you did not apply for the "guru" access level yet, it is time to apply for it on our [registration portal](https://bianca.science.uu.nl/auth/register/){:target="_blank"}. If using workshop credentials, you will have "guru" access already.*
+**Note** *that fine-tuning the parameters of the web server to covalently dock a ligand requires the most advanced privilege on the web server. If you did not apply for the "guru" access level yet, it is time to apply for it on our [registration portal](https://wenmr.science.uu.nl/auth/register/){:target="_blank"}. If using workshop credentials, you will have "guru" access already.*
A problem when trying to "covalently dock" a small ligand is that the van der Waals interactions will typically prevent close proximity of the atoms involved in the covalent bond.
To allow the distance restraint to be satisfied, we need to scale down the non-bonded interactions between the specific atoms involved in that covalent bond. For this purpose we created a special Cysteine residue (residue name: CYC), without hydrgogen atom on the sulfur and with significantly reduced VDW parameters for the sulfur atom (scaled down by a factor 10).
diff --git a/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md
index b0b7c971..50cb7ee6 100644
--- a/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md
+++ b/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md
@@ -925,7 +925,7 @@ docking calculations in `../../tutorial_files/cluster_analysis/clusters_ready/`.
## Protein-ligand docking with HADDOCK
-> Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the "guru" access level yet, it is time to apply for it via our [registration portal](https://bianca.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
+> Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the "guru" access level yet, it is time to apply for it via our [registration portal](https://wenmr.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
#### Setting up a new docking run targeting the identified binding pocket
diff --git a/education/biomolecular-simulations-2019/HADDOCK_tutorial/index.md b/education/biomolecular-simulations-2019/HADDOCK_tutorial/index.md
index 3d6e1e59..35d0dd3d 100644
--- a/education/biomolecular-simulations-2019/HADDOCK_tutorial/index.md
+++ b/education/biomolecular-simulations-2019/HADDOCK_tutorial/index.md
@@ -38,7 +38,7 @@ instructions and/or PyMOL commands.
In order to run this tutorial you will need to have the following software installed: [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 our [registration page](https://bianca.science.uu.nl/auth/register/){: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 our [registration page](https://wenmr.science.uu.nl/auth/register/){:target="_blank"}.
@@ -292,7 +292,7 @@ or download it from [here](./media/unambig.tbl){:target="_blank"} for convenienc
## Submit your docking run
-**Note** that fine-tuning the parameters of the web server to covalently dock a ligand requires the most advanced privilege on the web server. If you did not apply for the “guru” access level yet, it is time to apply for it on our [registration portal](https://bianca.science.uu.nl/auth/register/). If using workshop credentials, you will have “guru” access already.
+**Note** that fine-tuning the parameters of the web server to covalently dock a ligand requires the most advanced privilege on the web server. If you did not apply for the “guru” access level yet, it is time to apply for it on our [registration portal](https://wenmr.science.uu.nl/auth/register/). If using workshop credentials, you will have “guru” access already.
A problem when trying to "covalently dock" a small ligand is that the van der Waals interactions will typically prevent close proximity of the atoms involved in the covalent bond.
To allow the distance restraint to be satisfied, we need to scale down the non-bonded interactions between the specific atoms involved in that covalent bond. For this purpose we created a special Cysteine residue (residue name: CYC), without hydrgogen atom on the sulfur and with significantly reduced VDW parameters for the sulfur atom (scaled down by a factor 10).
diff --git a/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md
index 0e606f63..2ce319b3 100644
--- a/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md
+++ b/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md
@@ -840,7 +840,7 @@ Type 1 and the cluster analysis will start.
## Protein-ligand docking with HADDOCK
-Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the _guru_ access level yet, it is time to apply for it via our [registration portal](https://bianca.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
+Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the _guru_ access level yet, it is time to apply for it via our [registration portal](https://wenmr.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
#### Setting up a new docking run targeting the identified binding pocket
diff --git a/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md
index 6d85a073..3399f1c0 100644
--- a/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md
+++ b/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md
@@ -810,7 +810,7 @@ Otherwise, you can go to the next section of this tutorial, where These clusters
## Protein-ligand docking with HADDOCK
-Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the _guru_ access level yet, it is time to apply for it via our [registration portal](https://bianca.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
+Note that protein-ligand HADDOCKing typically requires fine-tuning a handful of parameters that requires the most advanced privilege on the web server. If you did not apply for the _guru_ access level yet, it is time to apply for it via our [registration portal](https://wenmr.science.uu.nl/auth/register/). Alternatively, you can use the course credentials that were provided to you during the summer school to submit your docking runs. Please, use the pre-calculated runs to move on with the analysis section.
#### Setting up a new docking run targeting the identified binding pocket
diff --git a/education/research-projects/index.md b/education/research-projects/index.md
index 5bb9e6b9..239fd44a 100644
--- a/education/research-projects/index.md
+++ b/education/research-projects/index.md
@@ -20,7 +20,7 @@ Contact person: Prof. Dr. A.M.J.J. Bonvin (a.m.j.j.bonvin@uu.nl)
### Introduction
The fact that an entire genome can nowadays be sequenced for less than $1,000 led to a boom in genetic information, which in turn attracted particular attention to biomolecular interactions. It is estimated that a human cell is regulated by over 300,000 protein interactions, but only a small fraction of these have been structurally characterized by experimental methods such as X-ray crystallography or Nuclear Magnetic Resonance (NMR) spectroscopy. Other biochemical and biophysical methods can, however, obtain partial structural information on these interactions, while bioinformatics analysis of the can also contribute important evolutionary data. Combining these predictions and/or partial experimental information with methods for structure prediction of interactions – docking – allows the generation of atomic structural models that complement the experimental techniques.
-All docking methods share three common elements: first, three-dimensional (3D) structural models of the individual components must be available; second, they must explore the conformational landscape of the interaction and generate candidate structural models of the complex, what is called sampling; finally, they must assess the generated models and select those that are more likely to be representatives of the native complex, what is called scoring. We have developed for this purpose an information-driven docking approach called HADDOCK ([https://www.bonvinlab.org](https://www.bonvinlab.org/software/haddock2.4){:target="_blank"} ). HADDOCK is also available as a [webserver](https://bianca.science.uu.nl){:target="_blank"}, together with several other services operated by our group. The server is used by more than 18,500 users [worldwide](https://bianca.science.uu.nl/user_map){:target="_blank"}. It currently is one of the best docking methods in the world as assessed in a blind international competition. HADDOCK is unique because it can use external information to bias the sampling towards the ‘right’ answer. Nevertheless, there are still many challenges related to describing larger and more complex systems, improving our protocols to handle different types of molecules, improving our scoring functions and assessing the impact of a variety of data and energy functions on the prediction performance.
+All docking methods share three common elements: first, three-dimensional (3D) structural models of the individual components must be available; second, they must explore the conformational landscape of the interaction and generate candidate structural models of the complex, what is called sampling; finally, they must assess the generated models and select those that are more likely to be representatives of the native complex, what is called scoring. We have developed for this purpose an information-driven docking approach called HADDOCK ([https://www.bonvinlab.org](https://www.bonvinlab.org/software/haddock2.4){:target="_blank"} ). HADDOCK is also available as a [webserver](https://wenmr.science.uu.nl){:target="_blank"}, together with several other services operated by our group. The server is used by more than 18,500 users [worldwide](https://wenmr.science.uu.nl/user_map){:target="_blank"}. It currently is one of the best docking methods in the world as assessed in a blind international competition. HADDOCK is unique because it can use external information to bias the sampling towards the ‘right’ answer. Nevertheless, there are still many challenges related to describing larger and more complex systems, improving our protocols to handle different types of molecules, improving our scoring functions and assessing the impact of a variety of data and energy functions on the prediction performance.
diff --git a/software/bpg/analysis.md b/software/bpg/analysis.md
index 6693a614..4c858223 100644
--- a/software/bpg/analysis.md
+++ b/software/bpg/analysis.md
@@ -77,7 +77,7 @@ table, th, td {
## [Advanced model refinement](/software/haddock2.4/tips/advanced_refinement/)
-The HADDOCK2.4 server provides a dedicated web interface to run a [refinement on a molecular complex](https://bianca.science.uu.nl/haddock2.4/refinement/1) (still experimental). As input, only a PDB file for each partner of the complex is needed. In case one wants to tune the default parameters, it is possible to run the refinement also locally or using the regular [submission interface](https://wenmr.science.uu.nl/haddock2.4/submit/1). Then following settings need to be adjusted:
+The HADDOCK2.4 server provides a dedicated web interface to run a [refinement on a molecular complex](https://wenmr.science.uu.nl/haddock2.4/refinement/1) (still experimental). As input, only a PDB file for each partner of the complex is needed. In case one wants to tune the default parameters, it is possible to run the refinement also locally or using the regular [submission interface](https://wenmr.science.uu.nl/haddock2.4/submit/1). Then following settings need to be adjusted:
### Settings to run water refinement locally
diff --git a/software/bpg/restraints.md b/software/bpg/restraints.md
index 5569a391..c5647052 100644
--- a/software/bpg/restraints.md
+++ b/software/bpg/restraints.md
@@ -164,7 +164,7 @@ More about optimal settings for different docking scenarios can be found [here](
# Getting restraints HADDOCK-ready
-In [HADDOCK2.4 webserver](https://bianca.science.uu.nl/haddock2.4/) active and passive residues can be entered manually or in a *tbl* file of ambiguous and unambiguous restraints.
+In [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4/) active and passive residues can be entered manually or in a *tbl* file of ambiguous and unambiguous restraints.
Such restraints file can be generated in the [GenTBL server](https://alcazar.science.uu.nl/services/GenTBL/) and can be further used when using HADDOCK locally, since it is already CNS-formatted.
@@ -214,9 +214,9 @@ Tutorials using CPORT:
* [HADDOCKing of the p53 N-terminal peptide to MDM2](/education/molmod/docking/)
-## [DISVIS](https://bianca.science.uu.nl/disvis/)
+## [DISVIS](https://wenmr.science.uu.nl/disvis/)
-[DISVIS](https://bianca.science.uu.nl/disvis/) visualizes and quantifies the information content of distance restraints between macromolecular complexes.
+[DISVIS](https://wenmr.science.uu.nl/disvis/) visualizes and quantifies the information content of distance restraints between macromolecular complexes.
Tutorial describing DisVis:
diff --git a/software/bpg/structures.md b/software/bpg/structures.md
index 9c00a61a..d34ec29b 100644
--- a/software/bpg/structures.md
+++ b/software/bpg/structures.md
@@ -137,11 +137,11 @@ Examples of using MD for HADDOCK are shown here:
Upon acquiring the input structures provided you might want to modify in one way or the other. This might not be very straightforward since pdb files have to meet strict formatting requirements and are rather lengthy to edit manually. The HADDOCK group has therefore developed a pipeline called PDB-Tools where pdb files can be submitted and edited it as needed. PDB-tools are available here:
-* [PDB-Tools Web](https://bianca.science.uu.nl/pdbtools/)
+* [PDB-Tools Web](https://wenmr.science.uu.nl/pdbtools/)
* [Local version of PDB-Tools](http://www.bonvinlab.org/pdb-tools/)
-[](https://bianca.science.uu.nl/pdbtools/)
+[](https://wenmr.science.uu.nl/pdbtools/)
Tutorials:
diff --git a/software/haddock2.4/airs.md b/software/haddock2.4/airs.md
index ae198764..5d9d6f6b 100644
--- a/software/haddock2.4/airs.md
+++ b/software/haddock2.4/airs.md
@@ -29,7 +29,7 @@ In the definition of those residues, one distinguishes between ***"active"*** an
## Use of bioinformatic interface predictions
-In absence of any experimental information on the interaction surfaces, you might want to try to predict them based on sequence conservation and other properties. We have developed for this purpose interface prediction software called [WHISCY](https://bianca.science.uu.nl/whiscy){:target="_blank"} and [CPORT](https://alcazar.science.uu.nl/services/CPORT){:target="_blank"}. They have been designed to provide an easy interface to HADDOCK and will output, among others, lists of active and passive residues for HADDOCK. CPORT is a meta predictor that integrates results from various other servers. Many others such predictors do exist!
+In absence of any experimental information on the interaction surfaces, you might want to try to predict them based on sequence conservation and other properties. We have developed for this purpose interface prediction software called [WHISCY](https://wenmr.science.uu.nl/whiscy){:target="_blank"} and [CPORT](https://alcazar.science.uu.nl/services/CPORT){:target="_blank"}. They have been designed to provide an easy interface to HADDOCK and will output, among others, lists of active and passive residues for HADDOCK. CPORT is a meta predictor that integrates results from various other servers. Many others such predictors do exist!
For more information refer to:
diff --git a/software/bpg/analysis.md b/software/bpg/analysis.md
index 6693a614..4c858223 100644
--- a/software/bpg/analysis.md
+++ b/software/bpg/analysis.md
@@ -77,7 +77,7 @@ table, th, td {
## [Advanced model refinement](/software/haddock2.4/tips/advanced_refinement/)
-The HADDOCK2.4 server provides a dedicated web interface to run a [refinement on a molecular complex](https://bianca.science.uu.nl/haddock2.4/refinement/1) (still experimental). As input, only a PDB file for each partner of the complex is needed. In case one wants to tune the default parameters, it is possible to run the refinement also locally or using the regular [submission interface](https://wenmr.science.uu.nl/haddock2.4/submit/1). Then following settings need to be adjusted:
+The HADDOCK2.4 server provides a dedicated web interface to run a [refinement on a molecular complex](https://wenmr.science.uu.nl/haddock2.4/refinement/1) (still experimental). As input, only a PDB file for each partner of the complex is needed. In case one wants to tune the default parameters, it is possible to run the refinement also locally or using the regular [submission interface](https://wenmr.science.uu.nl/haddock2.4/submit/1). Then following settings need to be adjusted:
### Settings to run water refinement locally
diff --git a/software/bpg/restraints.md b/software/bpg/restraints.md
index 5569a391..c5647052 100644
--- a/software/bpg/restraints.md
+++ b/software/bpg/restraints.md
@@ -164,7 +164,7 @@ More about optimal settings for different docking scenarios can be found [here](
# Getting restraints HADDOCK-ready
-In [HADDOCK2.4 webserver](https://bianca.science.uu.nl/haddock2.4/) active and passive residues can be entered manually or in a *tbl* file of ambiguous and unambiguous restraints.
+In [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4/) active and passive residues can be entered manually or in a *tbl* file of ambiguous and unambiguous restraints.
Such restraints file can be generated in the [GenTBL server](https://alcazar.science.uu.nl/services/GenTBL/) and can be further used when using HADDOCK locally, since it is already CNS-formatted.
@@ -214,9 +214,9 @@ Tutorials using CPORT:
* [HADDOCKing of the p53 N-terminal peptide to MDM2](/education/molmod/docking/)
-## [DISVIS](https://bianca.science.uu.nl/disvis/)
+## [DISVIS](https://wenmr.science.uu.nl/disvis/)
-[DISVIS](https://bianca.science.uu.nl/disvis/) visualizes and quantifies the information content of distance restraints between macromolecular complexes.
+[DISVIS](https://wenmr.science.uu.nl/disvis/) visualizes and quantifies the information content of distance restraints between macromolecular complexes.
Tutorial describing DisVis:
diff --git a/software/bpg/structures.md b/software/bpg/structures.md
index 9c00a61a..d34ec29b 100644
--- a/software/bpg/structures.md
+++ b/software/bpg/structures.md
@@ -137,11 +137,11 @@ Examples of using MD for HADDOCK are shown here:
Upon acquiring the input structures provided you might want to modify in one way or the other. This might not be very straightforward since pdb files have to meet strict formatting requirements and are rather lengthy to edit manually. The HADDOCK group has therefore developed a pipeline called PDB-Tools where pdb files can be submitted and edited it as needed. PDB-tools are available here:
-* [PDB-Tools Web](https://bianca.science.uu.nl/pdbtools/)
+* [PDB-Tools Web](https://wenmr.science.uu.nl/pdbtools/)
* [Local version of PDB-Tools](http://www.bonvinlab.org/pdb-tools/)
-[
](https://bianca.science.uu.nl/pdbtools/)
+[