Updated reference to HADDOCK2.4 server

haddocking · Aug 20, 2024 · 2387dea · 2387dea
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diff --git a/education/HADDOCK24/HADDOCK24-CACA-guided/index.md b/education/HADDOCK24/HADDOCK24-CACA-guided/index.md
@@ -27,13 +27,13 @@ For this tutorial we will make use the following web servers:
 
 * [HADDOCK2.4](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}: The HADDOCK web portal which allows to model 3D structures of the query complex using distance restraints derived by PS-HomPPI v2.0 to guide the docking.
 
+* 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).
 
-A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2/){:target="_blank"} can be found in the following publications:
+
+A description of the template-based modelling procedure described in this tutorial can be found in the following publication:
 
 * Li C Xue, João P G L M Rodrigues, Drena Dobbs, Vasant Honavar, Alexandre M J J Bonvin. [Template-based protein–protein docking exploiting pairwise interfacial residue restraints.](https://academic.oup.com/bib/article/18/3/458/2562753){:target="_blank"} _Briefings in bioinformatics_ *18*, 458-466 (2017).
 
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html){:target="_blank"} _Nature Protocols_, *5*, 883-897 (2010).
 
 Throughout the tutorial, colored text will be used to refer to questions or
 instructions, and/or PyMOL commands.

diff --git a/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md b/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
@@ -21,16 +21,8 @@ This tutorial will demonstrate the use of HADDOCK for predicting target70 of the
 
 For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4).
 
+* 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).
 
-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:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014).
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html)
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version <a href="https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html">here</a>.
 
 Further, multi-body docking and the use of symmetry restraints is described in the following paper:
 

diff --git a/education/HADDOCK24/HADDOCK24-DNA-small-molecule/index.md b/education/HADDOCK24/HADDOCK24-DNA-small-molecule/index.md
@@ -23,15 +23,7 @@ For this tutorial, we will predict the Netropsin/d(GGCCAATTGG) binding mode with
 
 For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}.
 
-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:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014){:target="_blank"}.
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html){:target="_blank"}
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version <a href="https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html">here</a>.
+* 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).
 
 
 Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands.

diff --git a/education/HADDOCK24/HADDOCK24-Xlinks/index.md b/education/HADDOCK24/HADDOCK24-Xlinks/index.md
@@ -28,15 +28,8 @@ satisfying the cross-links. This is an additional information which might be use
 We will thus be making use of the results of the [DisVis tutorial](/education/Others/disvis-webserver) to setup various
 docking runs using our [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4).
 
-A description of our 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:
+* 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).
 
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014).
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html)
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version <a href="https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html">here</a>.
 
 Throughout the tutorial, colored text will be used to refer to questions or
 instructions, and/or PyMOL commands.

diff --git a/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md b/education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md
@@ -35,15 +35,7 @@ In this tutorial we will be working with  Interleukin-1β (IL-1β) (PDB code [4I
 
 We will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}.
 
-A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2){:target="_blank"} can be found in the following publications:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014){:target="_blank"}.
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html){:target="_blank"}
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version [here](https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html){:target="_blank"}.
+* 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).
 
 
 
@@ -164,7 +156,7 @@ color red, paratope<br>
 
 <a class="prompt prompt-question">Can you identify the H3 loop? H stands for heavy chain (the first domain in our case with lower residue numbering). H3 is typically the longest loop.</a>
 
-Let's now switch to a surface representation to inspect the predicted binding site.
+Let us now switch to a surface representation to inspect the predicted binding site.
 
 <a class="prompt prompt-pymol">
 show surface<br>
@@ -359,7 +351,7 @@ The page will automatically refresh and the results will appear upon completion
 
 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). When special course credentials, the number of models generated will have been automatically decreased (250/50/50) to allow the runs to complete within a reasonable amount of time.
 
-In case you don't want to wait for your runs to be finished, a precalculated run can be found [here](https://wenmr.science.uu.nl/haddock2.4/result/4242424242/184871-4G6M-Ab-Ag-NMR-Ab-no-passive){:target="_blank"}.
+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/4242424242/184871-4G6M-Ab-Ag-NMR-Ab-no-passive){:target="_blank"}.
 
 
 <a class="prompt prompt-question">Inspect the result page</a>
@@ -424,7 +416,7 @@ hide lines<br>
 color yellow, 4G6M-matched<br>
 </a>
 
-Let's then superimpose all models on chain A (receptor) of the first model and calculate RMSD of chain B (ligand):
+Let us then superimpose all models on chain A (receptor) of the first model and calculate RMSD of chain B (ligand):
 
 
 <a class="prompt prompt-pymol">

diff --git a/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md b/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md
@@ -36,15 +36,7 @@ In this tutorial we will be working with  Interleukin-1β (IL-1β) (PDB code [4I
 
 For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}, [ProABC-2](https://wenmr.science.uu.nl/proabc2){:target="_blank"} and [PDB-tools webserver](https://wenmr.science.uu.nl/pdbtools){:target="_blank"}.
 
-A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2){:target="_blank"} can be found in the following publications:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014){:target="_blank"}.
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html){:target="_blank"}
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version [here](https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html){:target="_blank"}.
+* 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).
 
 
 ProABC-2 is described here:

diff --git a/education/HADDOCK24/HADDOCK24-binding-sites/index.md b/education/HADDOCK24/HADDOCK24-binding-sites/index.md
@@ -41,15 +41,7 @@ In the first part of this tutorial you will learn to clean and manipulate PDB fi
 
 For this tutorial we 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:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014).
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html)
-_Nature Protocols_, *5*, 883-897 (2010).
+* 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).
 
 
 Throughout the tutorial, coloured text will be used to refer to questions or

diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md
@@ -78,6 +78,8 @@ 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).
+
 #### Tutorial data set
 
 In this tutorial you will perform a protein-DNA docking using the bacteriophage 434 Cro repressor protein and the OR1 operator as an example case. All the tutorial data are made available as a *gzipped* tar archive (.tgz) in the following address [https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz](https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz). 

diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md
@@ -47,6 +47,15 @@ You should be able to go through this tutorial in about 1 hour.
 We will be using the [PBD-tools webserver](https://wenmr.science.uu.nl/pdbtools) for preprocessing a PDB file (optional) and the HADDOCK 2.4 webserver
  [https://wenmr.science.uu.nl/haddock2.4/](https://wenmr.science.uu.nl/haddock2.4/) to perform the docking.
 
+* 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).
+
+Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands.
+
+<a class="prompt prompt-question">This is a question prompt: try answering it!</a>
+<a class="prompt prompt-info">This an instruction prompt: follow it!</a>
+<a class="prompt prompt-pymol">This is a PyMOL prompt: write this in the PyMOL command line prompt!</a>
+
+
 ### Tutorial data set
 
 In this tutorial you will perform a protein-DNA docking using the bacteriophage 434 Cro repressor protein and the OR1 operator as an example case.

diff --git a/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md
@@ -19,15 +19,7 @@ This tutorial will demonstrate the use of HADDOCK for predicting the structure o
 
 For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}.
 
-A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2/){:target="_blank"} can be found in the following publications:
-
-* G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and  A.M.J.J. Bonvin.
-[The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](https://doi.org/doi:10.1016/j.jmb.2015.09.014){:target="_blank"}.
-_J. Mol. Biol._, *428*, 720-725 (2015).
-
-* S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin.
-[The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html){:target="_blank"}
-_Nature Protocols_, *5*, 883-897 (2010).  Download the final author version <a href="https://igitur-archive.library.uu.nl/chem/2011-0314-200252/UUindex.html">here</a>.
+* 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).
 
 
 Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands.