Merge pull request #720 from haddocking/rearrange-tutorials

Reordering of haddock3 tutorials

Author: VGPReys

education/HADDOCK3/index.md

@@ -6,35 +6,74 @@ image:
   feature: pages/banner_education-thin.jpg
 ---
 In this page you can find links to tutorials on the usage of the new modular HADDOCK3 version. HADDOCK3 has been and is developed under
-the umbrella of the [BioExcel Center of Excellence for Computational Biomolecular Research](https://www.bioexcel.eu){:target="_blank"} and in collaboration with the [Netherlands e-Science Center](){:target="_blank"}. 
+the umbrella of the [BioExcel Center of Excellence for Computational Biomolecular Research](https://www.bioexcel.eu){:target="_blank"} and in collaboration with the [Netherlands e-Science Center](https://www.esciencecenter.nl/){:target="_blank"}. 
 
 _Note that HADDOCK3 is still in heavy development and as such the software is evolving quickly._
 
 <hr>
 
-* [**HADDOCK3 documentation**](https://www.bonvinlab.org/haddock3)
-  Documentation for HADDOCK3 including [installation instructions](https://www.bonvinlab.org/haddock3/INSTALL.html){:target="_blank"}.
+# Getting started
 
-* [**HADDOCK3 user manual**](https://www.bonvinlab.org/haddock3-user-manual/)
-  User manual for HADDOCK3, with a comprehensive description of the software and its features, including a [Best Practices](https://www.bonvinlab.org/haddock3-user-manual/bpg.html){:target="_blank"} section and descriptions of several [HADDOCK docking scenarios](https://www.bonvinlab.org/haddock3-user-manual/docking_scenarios.html){:target="_blank"}.
+* **Online lectures**:
+  These two recordings of HADDOCK lectures explain basis of HADDOCK, ambiguous interaction restraints and introduce HADDOCK3 (*by Prof. Bonvin (June 7th, 2021) at the [BioExcel](https://www.bioexcel.eu){:target="_blank"} summerschool*):
 
-* [**HADDOCK restraints generation**](https://www.bonvinlab.org/haddock-restraints/home.html){:target="_blank"}:
-  A guide for the `haddock-restraints` tool allowing to generate various types of distance restraints for use in HADDOCK, also available via [a graphical user interface](http://wenmr.science.uu.nl/new/haddock-restraints){:target="_blank"}.
+  <ul>
+  <details>
+  <summary>Click here to view recorded lecture Part I (46 min.)
+  </summary>
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/N2Sr4qtRKhs" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> 
+  </details>
+  <br>
+  </ul>
+  <ul>
+  <details>
+  <summary>Click here to view recorded lecture Part II (43 min.)
+  </summary>
+     <iframe width="560" height="315" src="https://www.youtube.com/embed/qpx6bQZhWrU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+  </details>
+  <br>
+  </ul>
+
+* [**Basic docking run with HADDOCK3**](/education/HADDOCK3/HADDOCK3-antibody-antigen):
+  This tutorial describes a full step-by-step process from preparing the files for the docking, to the interpretation of the results. It is a good idea to go through it to get a basic introduction to HADDOCK3.
+
+<hr>
+
+# System-specific basic tutorials
 
-* [**HADDOCK3 antibody-antigen docking**](/education/HADDOCK3/HADDOCK3-antibody-antigen):
+* [**Antibody-antigen docking**](/education/HADDOCK3/HADDOCK3-antibody-antigen):
   This tutorial demonstrates the use of HADDOCK3 for predicting the structure of an antibody-antigen complex using information
   about the hypervariable loops of the antibody and a loose definition of the epitope determined through NMR experiments.
   As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.
 
-* [**HADDOCK3 nanobody-antigen docking**](/education/HADDOCK3/HADDOCK3-nanobody-antigen):
+* [**Nanobody-antigen docking**](/education/HADDOCK3/HADDOCK3-nanobody-antigen):
   This tutorial is similar to the antibody-antigen docking tutorial, but it uses a nanobody instead of an antibody. In the tutorial we explain how to generate an ensemble of nanobody conformations in their unbound form and then how to dock it to the antigen using HADDOCK3.
 
-* [**HADDOCK3 protein-glycan modelling and docking**](/education/HADDOCK3/HADDOCK3-protein-glycan):
+* [**Protein-Glycan modelling and docking**](/education/HADDOCK3/HADDOCK3-protein-glycan):
   This tutorial shows how to use HADDOCK3 to dock a glycan to a protein, provided that some information exists about the protein binding site.
   As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.
 
-* [**HADDOCK3 basic protein-DNA docking tutorial**](/education/HADDOCK3/HADDOCK3-protein-DNA-basic):
+* [**Protein-DNA docking tutorial**](/education/HADDOCK3/HADDOCK3-protein-DNA-basic):
   This tutorial demonstrates the use of Haddock3 for predicting the structure of a protein-DNA complex in which two protein units bind 
   to the double-stranded DNA in a symmetrical manner (reference structure [3CRO](https://www.rcsb.org/structure/3CRO)).
   In addition to provided ambiguous restraints used to drive the docking, symmetry restraints are also defined to enforce symmetrical binding to the protein.
   As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.
+
+<hr>
+
+# Advanced tutorials
+
+*coming soon*
+
+<hr>
+
+# Documentations
+
+* [**HADDOCK3 user manual**](https://www.bonvinlab.org/haddock3-user-manual/)
+  User manual for HADDOCK3, with a comprehensive description of the software and its features, including a [Best Practices](https://www.bonvinlab.org/haddock3-user-manual/bpg.html){:target="_blank"} section and descriptions of several [HADDOCK docking scenarios](https://www.bonvinlab.org/haddock3-user-manual/docking_scenarios.html){:target="_blank"}.
+
+* [**HADDOCK restraints generation**](https://www.bonvinlab.org/haddock-restraints/home.html){:target="_blank"}:
+  A guide for the `haddock-restraints` tool allowing to generate various types of distance restraints for use in HADDOCK, also available via [a graphical user interface](http://wenmr.science.uu.nl/haddock-restraints){:target="_blank"}.
+
+* [**HADDOCK3 software documentation**](https://www.bonvinlab.org/haddock3)
+  Documentation for HADDOCK3 including [installation instructions](https://www.bonvinlab.org/haddock3/INSTALL.html){:target="_blank"}.