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Jul 14, 2025
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add logic to make citations re-usable #717

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2174f82
add `publications.yml`
rvhonorato Jul 11, 2025
cc9093b
add `paper_citation.html`
rvhonorato Jul 11, 2025
1dc1762
add reusable references
rvhonorato Jul 11, 2025
8bbe7f5
update publication data
rvhonorato Jul 11, 2025
b228d45
Merge branch 'master' into 716-update-of-the-haddock24-server-referen…
rvhonorato Jul 14, 2025
1875ac7
tweaks
rvhonorato Jul 14, 2025
f5ba808
remove `**`
rvhonorato Jul 14, 2025
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8 changes: 8 additions & 0 deletions _data/publications.yml
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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
5 changes: 5 additions & 0 deletions _includes/paper_citation.html
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{% 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 }})
4 changes: 1 addition & 3 deletions education/HADDOCK/HADDOCK-Xlinks/index.md
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Expand Up @@ -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).
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-CACA-guided/index.md
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-DNA-small-molecule/index.md
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Expand Up @@ -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.
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3 changes: 1 addition & 2 deletions education/HADDOCK24/HADDOCK24-Xlinks/index.md
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Expand Up @@ -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.
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3 changes: 1 addition & 2 deletions education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-antibody-antigen/index.md
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-binding-sites/index.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md
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Expand Up @@ -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.

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2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion education/HADDOCK24/LightDock-membrane-proteins/index.md
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Expand Up @@ -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:

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2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III-2022/index.md
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III-2024/index.md
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III/index.md
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Expand Up @@ -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.
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4 changes: 1 addition & 3 deletions education/HADDOCK24/XL-MS-oligomer/index.md
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Expand Up @@ -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:
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