diff --git a/_data/publications.yml b/_data/publications.yml new file mode 100644 index 000000000..6f264e854 --- /dev/null +++ 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 new file mode 100644 index 000000000..ce07b992e --- /dev/null +++ b/_includes/paper_citation.html @@ -0,0 +1,5 @@ +{% assign paper = site.data.publications[include.key] %} + +* {{ 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 index d8069e5af..76db4389d 100644 --- 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 index 3edc174d5..29b64aa48 100755 --- 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 index 44c9d04ec..4b9dfb521 100644 --- 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 index 27725b1d7..dadc41fdf 100644 --- 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 index 216c86399..d32f3f230 100644 --- 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 index 843b0bb52..02d9aa9c9 100644 --- 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 index faed3a8b2..ac81a0640 100644 --- 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 index c2fb00443..45d83f3bc 100644 --- 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 index d92bde7ba..363a98542 100644 --- 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 index 55f89e550..b04d53157 100644 --- 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 index f6686864e..8e7c7d52c 100644 --- 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 index 7b1737f85..b5d2a684b 100644 --- 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 index c7af808ab..ce00db907 100644 --- 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 index 9164cad31..06d28dbd9 100644 --- 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 index 45f566f61..248e45e76 100644 --- 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 index fd9a5b91f..7584d1431 100644 --- 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 index 29d194524..4d65d2a59 100644 --- a/education/HADDOCK24/shape-small-molecule/index.md +++ b/education/HADDOCK24/shape-small-molecule/index.md @@ -22,7 +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"}. -* 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 or terminal commands. diff --git a/software/haddock2.4/index.md b/software/haddock2.4/index.md index 12b0d2719..597fc1b05 100644 --- a/software/haddock2.4/index.md +++ b/software/haddock2.4/index.md @@ -82,7 +82,7 @@ The functionalities are the same as the 2.4 version (the online manual has not c * 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). -* 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" %} **_For additional citations when using specific modules see also our [publication page](./publications)_**. diff --git a/software/haddock2.4/publications.md b/software/haddock2.4/publications.md index 359299767..92cb23392 100644 --- a/software/haddock2.4/publications.md +++ b/software/haddock2.4/publications.md @@ -29,8 +29,7 @@ The original JACS paper, together with an introduction to the study of biomolecu **_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). - +{% include paper_citation.html key="haddock24" %} **_And, if used, cite depending on the type of data and setting used the following publications:_**