Merge pull request #717 from haddocking/716-update-of-the-haddock24-server-reference-which-is-no-longer-advanced-online-but-nature-prot-19-32193241-2024

rvhonorato · web-flow · commit 121f8f1683b7 · 2025-07-14T17:15:20.000+02:00
add logic to make citations re-usable
diff --git a/_data/publications.yml b/_data/publications.yml
@@ -0,0 +1,8 @@
+haddock24:
+  authors: "R.V. Honorato, M.E. Trellet, B. Jiménez-García, 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"
+  title: "The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes"
+  url: "https://www.nature.com/articles/s41596-024-01011-0"
+  journal: Nature Protoc
+  details: "19, 3219–3241"
+  doi: "10.1038/s41596-024-01011-0"
+  year: 2024
diff --git a/_includes/paper_citation.html b/_includes/paper_citation.html
@@ -0,0 +1,5 @@
+{% assign paper = site.data.publications[include.key] %}
+<!-- Define how the citation should be formatted -->
+* {{ paper.authors }} [{{ paper.title }}]({{ paper.url }}){:target="_blank"}.
+_{{ paper.journal }}_, {{ paper.details }} DOI: [{{ paper.doi
+}}](https://doi.org/{{ paper.doi }}){:target="_blank"} ({{ paper.year }})
diff --git a/education/HADDOCK/HADDOCK-Xlinks/index.md b/education/HADDOCK/HADDOCK-Xlinks/index.md
@@ -31,9 +31,7 @@ docking runs using our [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/servic
 
 A description of our web server can be found in the following publications:
 
-* R.V. Honorato, M.E. Trellet, B. Jiménez-García, 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).
+{% include paper_citation.html key="haddock24" %}
 
 * 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).
diff --git a/education/HADDOCK24/HADDOCK24-CACA-guided/index.md b/education/HADDOCK24/HADDOCK24-CACA-guided/index.md
@@ -27,7 +27,7 @@ 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 A description of the template-based modelling procedure described in this tutorial can be found in the following publication:
diff --git a/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md b/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
@@ -21,7 +21,7 @@ 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 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
@@ -23,7 +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"}.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 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
@@ -28,8 +28,7 @@ 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).
 
-* 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).
-
+{% include paper_citation.html key="haddock24" %}
 
 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
@@ -35,8 +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"}.
 
-* 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).
-
+{% include paper_citation.html key="haddock24" %}
 
 
 And our work on antibody antigen complexes is described in the following publications:
diff --git a/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md b/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md
@@ -36,7 +36,7 @@ In this tutorial we will be working with  Interleukin-1β (IL-1β) (PDB code [4I
 
 References:
 
-* 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._,  *19*, 3219–3241 (2024).
+{% include paper_citation.html key="haddock24" %}
 
 
 ProABC-2 is described here:
diff --git a/education/HADDOCK24/HADDOCK24-binding-sites/index.md b/education/HADDOCK24/HADDOCK24-binding-sites/index.md
@@ -41,7 +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).
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 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
@@ -78,7 +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).
+{% include paper_citation.html key="haddock24" %}
 
 #### Tutorial data set
 
diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md
@@ -47,7 +47,7 @@ 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).
+{% include paper_citation.html key="haddock24" %}
 
 Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands.
 
diff --git a/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md
@@ -19,7 +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"}.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands.
diff --git a/education/HADDOCK24/LightDock-membrane-proteins/index.md b/education/HADDOCK24/LightDock-membrane-proteins/index.md
@@ -32,7 +32,7 @@ In this tutorial we will be working with the crystal structure  of _Mus musculus
 
 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"}.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 The integrative approach followed in this tutorial is described here:
 
diff --git a/education/HADDOCK24/RNA-Pol-III-2022/index.md b/education/HADDOCK24/RNA-Pol-III-2022/index.md
@@ -32,7 +32,7 @@ During this tutorial, we pretend that the structure of the Pol III core (14 subu
 We will be making use of i) our [DISVIS server](https://wenmr.science.uu.nl/disvis/){:target="_blank"} to analyse the cross-links and detect possible false positives and ii) of the new [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"} to setup docking runs, using the coarse-graining option to speed up the calculations (especially needed due to the large size of the system). 
 As an alternative strategy, we will use our [PowerFit server][link-powerfit-web] to fit the largest components of the complex into the 9Å cryo-EM map and then use those as a starting point for the modelling of the remaining components.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 Throughout the tutorial, colored text will be used to refer to questions or
 instructions, and/or PyMOL commands.
diff --git a/education/HADDOCK24/RNA-Pol-III-2024/index.md b/education/HADDOCK24/RNA-Pol-III-2024/index.md
@@ -32,7 +32,7 @@ During this tutorial, we pretend that the structure of the Pol III core (14 subu
 We will be making use of i) our [DISVIS server](https://wenmr.science.uu.nl/disvis/){:target="_blank"} to analyse the cross-links and detect possible false positives and ii) of the new [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"} to setup docking runs, using the coarse-graining option to speed up the calculations (especially needed due to the large size of the system). 
 As an alternative strategy, we will use our [PowerFit server][link-powerfit-web]{:target="_blank"} to fit the largest components of the complex into the 9Å cryo-EM map and then use those as a starting point for the modelling of the remaining components.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 Throughout the tutorial, colored text will be used to refer to questions or
 instructions, and/or ChimeraX commands.
diff --git a/education/HADDOCK24/RNA-Pol-III/index.md b/education/HADDOCK24/RNA-Pol-III/index.md
@@ -32,7 +32,7 @@ During this tutorial, we pretend that the structure of the Pol 3 core (14 subuni
 We will be making use of i) our [DISVIS server](https://wenmr.science.uu.nl/disvis/){:target="_blank"} to analyse the cross-links and detect possible false positives and ii) of the new [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"} to setup docking runs, using the new coarse-graining option to speed up the calculations (especially needed due to the large size of the system). 
 As an alternative strategy, we will use our [PowerFIt server][link-powerfit-web] to fit the largest components of the complex into the 9Å cryo-EM map and then use those as starting point for the modelling of the remaining components.
 
-* 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).
+{% include paper_citation.html key="haddock24" %}
 
 Throughout the tutorial, colored text will be used to refer to questions or
 instructions, and/or PyMOL commands.
diff --git a/education/HADDOCK24/XL-MS-oligomer/index.md b/education/HADDOCK24/XL-MS-oligomer/index.md
@@ -46,9 +46,7 @@ _J. Mol. Biol._. *429(3)*, 399-407 (2016).
 [DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes](https://doi.org/doi:10.1093/bioinformatics/btv333){:target="_blank"}.
   _Bioinformatics_ *31*, 3222-3224 (2015).
 
-* R.V. Honorato, M.E. Trellet, B. Jiménez-García, 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).
+{% include paper_citation.html key="haddock24" %}
 
 
 Further, multi-body docking and the use of symmetry restraints is described in the following paper:
diff --git a/education/HADDOCK24/shape-small-molecule/index.md b/education/HADDOCK24/shape-small-molecule/index.md
diff --git a/software/haddock2.4/index.md b/software/haddock2.4/index.md
diff --git a/software/haddock2.4/publications.md b/software/haddock2.4/publications.md
