Merge pull request #714 from rvhonorato/gentbl

rvhonorato · web-flow · commit 0a7d916f962b · 2025-07-11T11:51:04.000+02:00
Update `GenTBL` links
diff --git a/education/HADDOCK/HADDOCK-binding-sites/index.md b/education/HADDOCK/HADDOCK-binding-sites/index.md
@@ -686,7 +686,7 @@ This will ensure that the ligand is properly drawn inside the binding pocket.
 2. For the subsequent flexible refinement stages, we define the binding pocket only as passive and the ligand as active. 
 This ensures that the ligand can explore the binding pocket.
 
-In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints: [https://alcazar.science.uu.nl/services/GenTBL/](https://alcazar.science.uu.nl/services/GenTBL/) (unfold the *Residue selection* menu):
+In order to create those two restraint files, use the `Generate Restraints` option from the  haddock-restraints tool accessible at [https://wenmr.science.uu.nl/haddock-restraints/](https://wenmr.science.uu.nl/haddock-restraints/):
 
 <a class="prompt prompt-info">
 Selection 1: Active residues (directly involved in the interaction) -> enter here the list of residues defining the binding site (see above)
diff --git a/education/HADDOCK24/HADDOCK24-binding-sites/index.md b/education/HADDOCK24/HADDOCK24-binding-sites/index.md
@@ -700,7 +700,7 @@ This will ensure that the ligand is properly drawn inside the binding pocket.
 2. For the subsequent flexible refinement stages, we define the binding pocket only as passive and the ligand as active.
 This ensures that the ligand can explore the binding pocket.
 
-In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints: [https://alcazar.science.uu.nl/services/GenTBL/](https://alcazar.science.uu.nl/services/GenTBL/) (unfold the *Residue selection* menu):
+In order to create those two restraint files, use the `Generate Restraints` from the haddock-restraints tool accessible at [https://wenmr.science.uu.nl/haddock-restraints/](https://wenmr.science.uu.nl/haddock-restraints/):
 
 <a class="prompt prompt-info">
 Selection 1: Active residues (directly involved in the interaction) -> enter here the list of residues defining the binding site (see above)
diff --git a/education/HADDOCK24/HADDOCK24-local-tutorial/index.md b/education/HADDOCK24/HADDOCK24-local-tutorial/index.md
@@ -641,7 +641,7 @@ The following command will return all residues with a relative SASA for either t
 </a>
 
 Once you have defined your active and passive residues for both molecules, you can proceed with the generation of the AIR restraint file for HADDOCK.
-For this you can either make use of our online [GenTBL](https://alcazar.science.uu.nl/services/GenTBL/){:target="_blank"} webserver, entering the list of active and passive residues for each molecule, and saving the resulting restraint list to a text file, or use another `haddock-tools` script.
+For this you can either make use of our online `Generate Restraints` [haddock-restraints](https://wenmr.science.uu.nl/haddock-restraints/){:target="_blank"} web service, entering the list of active and passive residues for each molecule, and saving the resulting restraint list to a text file, or use another `haddock-tools` script.
 
 To use our `haddock-tools` `active-passive-to-ambig.py` script you need to create for each molecule a file containing two lines:
 * The first line corresponds to the list of active residues (numbers separated by spaces)
diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md
@@ -78,7 +78,7 @@ You should be able to go through this tutorial in about 4 hours.
 Basic knowledge on the principles and use of HADDOCK is useful but not required.
 We will be using the HADDOCK 2.4 webserver [https://wenmr.science.uu.nl/haddock2.4/](https://wenmr.science.uu.nl/haddock2.4/) to perform the docking and the standalone version of HADDOCK to perform the analysis of the results.
 
-* R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys,  P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and **A.M.J.J. Bonvin**. [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes](https://www.nature.com/articles/s41596-024-01011-0.epdf?sharing_token=UHDrW9bNh3BqijxD2u9Xd9RgN0jAjWel9jnR3ZoTv0O8Cyf_B_3QikVaNIBRHxp9xyFsQ7dSV3t-kBtpCaFZWPfnuUnAtvRG_vkef9o4oWuhrOLGbBXJVlaaA9ALOULn6NjxbiqC2VkmpD2ZR_r-o0sgRZoHVz10JqIYOeus_nM%3D). _Nature Prot._, Advanced Online Publication DOI: 10.1038/s41596-024-01011-0 (2024).
+* R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys,  P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and **A.M.J.J. Bonvin**. [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes](https://www.nature.com/articles/s41596-024-01011-0.epdf?sharing_token=UHDrW9bNh3BqijxD2u9Xd9RgN0jAjWel9jnR3ZoTv0O8Cyf_B_3QikVaNIBRHxp9xyFsQ7dSV3t-kBtpCaFZWPfnuUnAtvRG_vkef9o4oWuhrOLGbBXJVlaaA9ALOULn6NjxbiqC2VkmpD2ZR_r-o0sgRZoHVz10JqIYOeus_nM%3D). _Nature Prot._, Advanced Online Publication DOI: 10.1038/s41596-024-01011-0 (2024).
 
 #### Tutorial data set
 
@@ -509,7 +509,8 @@ In this part, you will use a custom-made plugin for the `PyMol` molecular viewer
 This plugin (`AIRviewer.py`) comes as part of the tutorial data set, and you will be instructed on how to use it during the course of this part.
 The plugin combines the ability to construct custom restraint sets for multi-body systems with the convenience of a visual appreciation of the resulting restraints network. 
 
-An alternative to the use of this plugin is a special HADDOCK interface available at: [https://wenmr.science.uu.nl/gentbl/](https://wenmr.science.uu.nl/gentbl/)
+An alternative to the use of this plugin is a special HADDOCK `Generate Restraints` web interface available at: [https://wenmr.science.uu.nl/haddock-restraints/](https://wenmr.science.uu.nl/haddock-restraints/)
+
 
 #### Constructing AIRs for protein-DNA systems
 
diff --git a/education/HADDOCK24/HADDOCK24-protein-glycan/index.md b/education/HADDOCK24/HADDOCK24-protein-glycan/index.md
@@ -536,7 +536,7 @@ You can inspect the results of a precalculated run [here](https://rascar.science
 
 <!-- Links -->
 [air-help]: https://www.bonvinlab.org/software/haddock2.4/airs/ "AIRs help"
-[gentbl]: https://wenmr.science.uu.nl/gentbl/ "GenTBL"
+[haddock-restraints]: https://wenmr.science.uu.nl/haddock-restraints "haddock-restraints"
 [haddock24protein]: /education/HADDOCK24/HADDOCK24-protein-protein-basic/
 [haddock-repo]: https://github.com/haddocking/haddock3 "HADDOCK3 GitHub"
 [installation]: https://www.bonvinlab.org/haddock3/INSTALL.html "Installation"
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md
@@ -582,7 +582,7 @@ This is, however, not a hard limit, and you might consider including even more b
 ### Defining ambiguous restraints
 
 Once you have identified your active and passive residues for both molecules, you can proceed with the generation of the ambiguous interaction restraints (AIR) file for HADDOCK.
-For this you can either make use of our online [GenTBL][gentbl] web service, entering the list of active and passive residues for each molecule, 
+For this you can either make use of our online `Generate Restraints` [haddock-restraints][haddock-restraints] web service, entering the list of active and passive residues for each molecule, 
 the chainIDs of each molecule and saving the resulting restraint list to a text file, or use another `haddock3-restraints` sub-command.
 
 To use our `haddock3-restraints active_passive_to_ambig` script, you need to
@@ -2902,7 +2902,7 @@ And check also our [education](/education){:target="_blank"} web page where you
 
 <!-- Links -->
 [air-help]: https://www.bonvinlab.org/software/haddock2.4/airs/ "AIRs help"
-[gentbl]: https://wenmr.science.uu.nl/gentbl/ "GenTBL"
+[haddock-restraints]: https://wenmr.science.uu.nl/haddock-restraints/ "haddock-restraints"
 [haddock24protein]: /education/HADDOCK24/HADDOCK24-protein-protein-basic/
 [haddock-repo]: https://github.com/haddocking/haddock3 "HADDOCK3 GitHub"
 [haddock-tools]: https://github.com/haddocking/haddock-tools "HADDOCK tools GitHub"
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-BioExcel2024 b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-BioExcel2024
@@ -638,7 +638,7 @@ This is, however, not a hard limit, and you might consider including even more b
 ### Defining ambiguous restraints
 
 Once you have identified your active and passive residues for both molecules, you can proceed with the generation of the ambiguous interaction restraints (AIR) file for HADDOCK.
-For this you can either make use of our online [GenTBL][gentbl] web service, entering the list of active and passive residues for each molecule, 
+For this you can either make use of our online `Generate Restraints` [haddock-restraints][haddock-restraints] web service, entering the list of active and passive residues for each molecule, 
 the chainIDs of each molecule and saving the resulting restraint list to a text file, or use another `haddock3-restraints` sub-command.
 
 To use our `haddock3-restraints active_passive_to_ambig` script, you need to
@@ -2523,7 +2523,7 @@ And check also our [education](/education){:target="_blank"} web page where you
 
 <!-- Links -->
 [air-help]: https://www.bonvinlab.org/software/haddock2.4/airs/ "AIRs help"
-[gentbl]: https://wenmr.science.uu.nl/gentbl/ "GenTBL"
+[haddock-restraints]: https://wenmr.science.uu.nl/haddock-restraints/ "haddock-restraints"
 [haddock24protein]: /education/HADDOCK24/HADDOCK24-protein-protein-basic/
 [haddock-repo]: https://github.com/haddocking/haddock3 "HADDOCK3 GitHub"
 [haddock-tools]: https://github.com/haddocking/haddock-tools "HADDOCK tools GitHub"
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-Bratislava b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-Bratislava
@@ -585,7 +585,7 @@ important chemical group seems solvent accessible from a visual inspection.
 
 Once you have defined your active and passive residues for both molecules, you
 can proceed with the generation of the ambiguous interaction restraints (AIR) file for HADDOCK.
-For this you can either make use of our online [GenTBL][gentbl] web service, entering the
+For this you can either make use of our online `Generate Restraints` [haddock-restraints][haddock-restraints] web service, entering the
 list of active and passive residues for each molecule, and saving the resulting
 restraint list to a text file, or use the relevant `haddock3-restraints` command.
 
@@ -1517,7 +1517,7 @@ And check also our [education](/education) web page where you will find more tut
 
 <!-- Links -->
 [air-help]: https://www.bonvinlab.org/software/haddock2.4/airs/ "AIRs help"
-[gentbl]: https://wenmr.science.uu.nl/gentbl/ "GenTBL"
+[haddock-restraints]: https://wenmr.science.uu.nl/haddock-restraints "haddock-restraints"
 [haddock24protein]: /education/HADDOCK24/HADDOCK24-protein-protein-basic/
 [haddock-repo]: https://github.com/haddocking/haddock3 "HADDOCK3 GitHub"
 [haddock-tools]: https://github.com/haddocking/haddock-tools "HADDOCK tools GitHub"
diff --git a/education/HADDOCK3/HADDOCK3-protein-glycan/index.md b/education/HADDOCK3/HADDOCK3-protein-glycan/index.md
@@ -850,7 +850,7 @@ What is the impact of the change in the scoring weights on the ranking of the mo
 
 <!-- Links -->
 [air-help]: https://www.bonvinlab.org/software/haddock2.4/airs/ "AIRs help"
-[gentbl]: https://wenmr.science.uu.nl/gentbl/ "GenTBL"
+[haddock-restraints]: https://wenmr.science.uu.nl/haddock-restraints/ "haddock-restraints"
 [haddock24protein]: /education/HADDOCK24/HADDOCK24-protein-protein-basic/
 [haddock-repo]: https://github.com/haddocking/haddock3 "HADDOCK3 GitHub"
 [installation]: https://www.bonvinlab.org/haddock3/INSTALL.html "Installation"
diff --git a/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2018/Metadynamics_tutorial/index.md
@@ -938,7 +938,7 @@ This will ensure that the ligand is properly drawn inside the binding pocket.
 2. For the subsequent flexible refinement stages, we define the binding pocket only as passive and the ligand as active. 
 This ensures that the ligand can explore the binding pocket.
 
-In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints: [https://alcazar.science.uu.nl/services/GenTBL/](https://alcazar.science.uu.nl/services/GenTBL/) (unfold the *Residue selection* menu):
+In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints (in the Generate Restraints tab): [https://wenmr.science.uu.nl/haddock-restraints](https://wenmr.science.uu.nl/haddock-restraints/):
 
 <a class="prompt prompt-info">
 Selection 1: Active residues (directly involved in the interaction) -> enter here the list of residues defining the binding site
diff --git a/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md
@@ -853,7 +853,7 @@ This will ensure that the ligand is properly drawn inside the binding pocket.
 2. For the subsequent flexible refinement stages, we define the binding pocket only as passive and the ligand as active.
 This ensures that the ligand can explore the binding pocket.
 
-In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints: [https://alcazar.science.uu.nl/services/GenTBL/](https://alcazar.science.uu.nl/services/GenTBL/) (unfold the *Residue selection* menu):
+In order to create those two restraint files, use the `Generate Restraints` option from the haddock-restraints tool accessible at [https://wenmr.science.uu.nl/haddock-restraints](https://wenmr.science.uu.nl/haddock-restraints):
 
 <a class="prompt prompt-info">
 Selection 1: Active residues (directly involved in the interaction) -> enter here the list of residues defining the binding site:
diff --git a/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2020/Metadynamics_tutorial/index.md
@@ -823,7 +823,7 @@ This will ensure that the ligand is properly drawn inside the binding pocket.
 2. For the subsequent flexible refinement stages, we define the binding pocket only as passive and the ligand as active.
 This ensures that the ligand can explore the binding pocket.
 
-In order to create those two restraint files, use the HADDOCK server tool to generate AIR restraints: [https://alcazar.science.uu.nl/services/GenTBL/](https://alcazar.science.uu.nl/services/GenTBL/) (unfold the *Residue selection* menu):
+In order to create those two restraint files, use the `Generate Restraints` option from the haddock-restraints tool accessible at [https://wenmr.science.uu.nl/haddock-restraints/](https://wenmr.science.uu.nl/haddock-restraints/): 
 
 <a class="prompt prompt-info">
 Selection 1: Active residues (directly involved in the interaction) -> enter here the list of residues defining the binding site:
diff --git a/software/bpg/restraints.md b/software/bpg/restraints.md
@@ -166,7 +166,7 @@ More about optimal settings for different docking scenarios can be found [here](
 
 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.
+Such restraints file can be generated using the `Generate Restraints` from [haddock-restraints](https://wenmr.science.uu.nl/haddock-restraints) web service and can be further used when using HADDOCK locally, since it is already CNS-formatted.
 
 **[Haddock tools](https://github.com/haddocking/haddock-tools)** a bunch of useful tool available on [Github](https://github.com/haddocking/haddock-tools) a bunch of useful tool available on github for use with local version of HADDOCK.
 * *contact-chain*, *contact-segID* - programs to calculate all heavy atom interchain contacts within a given distance cutoff - useful to define active/passive residues based on a template structure
diff --git a/software/haddock2.2/haddock-start.html b/software/haddock2.2/haddock-start.html
@@ -14,7 +14,7 @@ <H2 align=right><FONT COLOR=RED>P</FONT>roject <FONT COLOR=RED>S</FONT>etup</H2>
 <HR>
 <TABLE>
 <TR rowspan=1 align="left">
-    <TD colspan=2><UL><LI><B><A TARGET=new HREF="https://alcazar.science.uu.nl/services/GenTBL">Generate AIR restraint file for multibody docking</A></B></TD>
+    <TD colspan=2><UL><LI><B><A TARGET=new HREF="https://wenmr.science.uu.nl/haddock-restraints">Generate AIR restraint file for multibody docking</A></B></TD>
 </TR>
 <TR rowspan=1 align="left">
     <TD colspan=1><UL><LI><B><A HREF="/software/haddock2.2/start_new">Start a new project</A></B></TD>
diff --git a/software/haddock2.4/airs.md b/software/haddock2.4/airs.md
@@ -192,7 +192,7 @@ To select the residues that satisfy the 40% accessibility cut-off type:
 <hr>
 ## Generating the AIR restraints file  
     
-Once you have defined your active and passive residues you can use our [online server](https://milou.science.uu.nl/services/GenTBL/){:target="_blank"} to generate a CNS-formatted ambiguous distance restraints file.
+Once you have defined your active and passive residues you can use our [online `Generate Restraints` service](https://wenmr.science.uu.nl/haddock-restraints){:target="_blank"} to generate a CNS-formatted ambiguous distance restraints file.
     
 "Copy and paste" the output or save it as a simple text to disk using "file save as". Make sure the saved file contains the proper data since some browsers might give problems with this service.
     
