Skip to content

add logic to make citations re-usable #717

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rvhonorato merged 7 commits into from
Jul 14, 2025
Merged

add logic to make citations re-usable #717

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 8 additions & 0 deletions _data/publications.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
5 changes: 5 additions & 0 deletions _includes/paper_citation.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{% assign paper = site.data.papers[include.key] %}
<!-- Define how the citation should be formatted -->
* {{ paper.authors }} [{{ paper.title }}]({{ paper.url }}). _{{ paper.journal
}}_, {{ paper.details }} DOI: [{{ paper.doi }}](https://doi.org/{{ paper.doi }})
({{ paper.year }})
4 changes: 1 addition & 3 deletions education/HADDOCK/HADDOCK-Xlinks/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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).
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-CACA-guided/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-DNA-small-molecule/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
3 changes: 1 addition & 2 deletions education/HADDOCK24/HADDOCK24-Xlinks/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
3 changes: 1 addition & 2 deletions education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-antibody-antigen/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-binding-sites/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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

Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.

Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/HADDOCK24-protein-protein-basic/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/LightDock-membrane-proteins/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:

Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III-2022/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III-2024/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
2 changes: 1 addition & 1 deletion education/HADDOCK24/RNA-Pol-III/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
4 changes: 1 addition & 3 deletions education/HADDOCK24/XL-MS-oligomer/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
Loading
Loading