From 2387dea68e1b8993e61e4aeb2a4406cf7582dc01 Mon Sep 17 00:00:00 2001 From: amjjbonvin Date: Tue, 20 Aug 2024 14:48:15 +0200 Subject: [PATCH] Updated reference to HADDOCK2.4 server --- .../HADDOCK24/HADDOCK24-CACA-guided/index.md | 6 +++--- .../HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md | 10 +--------- .../HADDOCK24-DNA-small-molecule/index.md | 10 +--------- education/HADDOCK24/HADDOCK24-Xlinks/index.md | 9 +-------- .../HADDOCK24-antibody-antigen-basic/index.md | 16 ++++------------ .../HADDOCK24-antibody-antigen/index.md | 10 +--------- .../HADDOCK24/HADDOCK24-binding-sites/index.md | 10 +--------- .../HADDOCK24-protein-DNA-advanced/index.md | 2 ++ .../HADDOCK24-protein-DNA-basic/index.md | 9 +++++++++ .../HADDOCK24-protein-protein-basic/index.md | 10 +--------- .../LightDock-membrane-proteins/index.md | 10 +--------- education/HADDOCK24/RNA-Pol-III-2022/index.md | 10 +--------- education/HADDOCK24/RNA-Pol-III/index.md | 10 +--------- education/HADDOCK24/XL-MS-oligomer/index.md | 10 ++-------- .../HADDOCK24/shape-small-molecule/index.md | 11 +---------- software/haddock2.4/index.md | 8 +++----- software/haddock2.4/publications.md | 5 +++++ 17 files changed, 38 insertions(+), 118 deletions(-) diff --git a/education/HADDOCK24/HADDOCK24-CACA-guided/index.md b/education/HADDOCK24/HADDOCK24-CACA-guided/index.md index 0a557f02..3edc174d 100755 --- 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 index 86a7ac50..44c9d04e 100644 --- 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 here. 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 index 63ab6871..27725b1d 100644 --- 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 here. +* 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 index abf4563d..216c8639 100644 --- 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 here. 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 index 12a52c2b..cb5e280f 100644 --- 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
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. -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. show surface
@@ -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"}. Inspect the result page @@ -424,7 +416,7 @@ hide lines
color yellow, 4G6M-matched
-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): diff --git a/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md b/education/HADDOCK24/HADDOCK24-antibody-antigen/index.md index 2d8c2681..e0134542 100644 --- 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 index 1fc92af0..645577f1 100644 --- 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 index 97483794..b4c5feec 100644 --- 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 index 433b0ab1..55f89e55 100644 --- 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. + +This is a question prompt: try answering it! +This an instruction prompt: follow it! +This is a PyMOL prompt: write this in the PyMOL command line prompt! + + ### 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 index b29ace5f..17886c4a 100644 --- 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 here. +* 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/LightDock-membrane-proteins/index.md b/education/HADDOCK24/LightDock-membrane-proteins/index.md index 02937d73..7b1737f8 100644 --- a/education/HADDOCK24/LightDock-membrane-proteins/index.md +++ b/education/HADDOCK24/LightDock-membrane-proteins/index.md @@ -32,15 +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"}. -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). 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 index 5014ee0b..104f7e62 100644 --- a/education/HADDOCK24/RNA-Pol-III-2022/index.md +++ b/education/HADDOCK24/RNA-Pol-III-2022/index.md @@ -32,15 +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. -A description of our the previous 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). +* 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, colored text will be used to refer to questions or instructions, and/or PyMOL commands. diff --git a/education/HADDOCK24/RNA-Pol-III/index.md b/education/HADDOCK24/RNA-Pol-III/index.md index 248397c0..45f566f6 100644 --- a/education/HADDOCK24/RNA-Pol-III/index.md +++ b/education/HADDOCK24/RNA-Pol-III/index.md @@ -32,15 +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. -A description of our the previous 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). +* 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, 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 index 3bfea552..88c43ee9 100644 --- a/education/HADDOCK24/XL-MS-oligomer/index.md +++ b/education/HADDOCK24/XL-MS-oligomer/index.md @@ -34,7 +34,7 @@ and imposing symmetry restraints to generate the proper homomeric complex. Those For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4). -A description of DisVis and 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: +A description of DisVis and of the HADDOCK2.4 web server can be found in the following publications: * G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin. [The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes.](https://doi.org/10.1016/j.jmb.2016.11.032){:target="_blank"}. @@ -44,13 +44,7 @@ _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). -* 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, 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(4)*, 720-725 (2016). - -* 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). 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 index c097089c..29d19452 100644 --- a/education/HADDOCK24/shape-small-molecule/index.md +++ b/education/HADDOCK24/shape-small-molecule/index.md @@ -22,16 +22,7 @@ can be seen in our freely-available [paper on JCIM](https://pubs.acs.org/doi/ful 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 here. +* 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 or terminal commands. diff --git a/software/haddock2.4/index.md b/software/haddock2.4/index.md index d4eeaf89..cf696f66 100644 --- a/software/haddock2.4/index.md +++ b/software/haddock2.4/index.md @@ -79,11 +79,9 @@ Fax: +31-30-2537623 **_When using HADDOCK cite:_** -* Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin. [HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.](https://doi.org/doi:10.1021/ja026939x) - _J. Am. Chem. Soc._ **125**, 1731-1737 (2003). +* Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin. [HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.](https://doi.org/doi:10.1021/ja026939x) _J. Am. Chem. Soc._ **125**, 1731-1737 (2003). -* 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 (2016). +* 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). **_For additional citations when using specific modules see also our [publication page](./publications)_**. @@ -91,7 +89,7 @@ Fax: +31-30-2537623 ### Acknowledgments: -HADDOCK is derived from [ARIA](https://aria.pasteur.fr) scripts by Michael Nilges and Jens Linge. +HADDOCK was originally derived from [ARIA](https://aria.pasteur.fr) scripts by Michael Nilges and Jens Linge. * J.P. Linge, M. Habeck, W. Rieping and M. Nilges (2003). [ARIA: automated NOE assignment and NMR structure calculation.](https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12538267&dopt=Abstract) _Bioinformatics_ **19**, 315-316. diff --git a/software/haddock2.4/publications.md b/software/haddock2.4/publications.md index 2736283a..35929976 100644 --- a/software/haddock2.4/publications.md +++ b/software/haddock2.4/publications.md @@ -27,6 +27,11 @@ The original JACS paper, together with an introduction to the study of biomolecu "[HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.](https://doi.org/doi:10.1002/prot.21723)" _Proteins: Struc. Funct. & Bioinformatic_ **69**, 726-733 (2007). +**_When using the HADDOCK2.4 web service cite:_** + +* 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). + + **_And, if used, cite depending on the type of data and setting used the following publications:_** The use of _residual dipolar couplings_ in HADDOCK is described in: