Regroup HADDOCK2.4 tutorials

education/HADDOCK24/index.md

@@ -1,29 +1,36 @@
 ---
 layout: page
-title: "HADDOCK Tutorials for version 2.4"
+title: "HADDOCK2.4 tutorials"
 tags: [MODELLER, GROMACS, HADDOCK, molecular dynamics, homology modelling, docking, p53, MDM2]
 image:
   feature: pages/banner_education-thin.jpg
 ---
-In this page you can find links to tutorials on the usage of our software and webportal [HADDOCK 2.4](https://wenmr.science.uu.nl/haddock2.4/){:target="_blank"}.
+In this page you can find links to tutorials on the usage of our web server [HADDOCK 2.4](https://wenmr.science.uu.nl/haddock2.4/){:target="_blank"} and command-line tool installation tutorial.
 
-* [**HADDOCK2.4 local installation tutorial**](/education/HADDOCK24/HADDOCK24-local-tutorial):
-  A tutorial demonstrating the installation and use of a local installation of HADDOCK2.4. It demonstrates various docking scenarios.
-  You will need for this a valid license of HADDOCK2.4.
+* table of contents
+{:toc}
 
-* [**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"}.
+<hr>
+
+# Getting started with HADDOCK web server
 
-* [**HADDOCK2.4 basic protein-protein docking tutorial**](/education/HADDOCK24/HADDOCK24-protein-protein-basic):
-  A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data.
+* [**Basic docking run with HADDOCK web server**](/education/HADDOCK24/HADDOCK24-protein-protein-basic):
+  A tutorial demonstrating a step-by-step use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data.
   This tutorial does not require any Linux expertise and only makes use of our web server and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
 
+# Basic web server tutorials
+
 * [**HADDOCK2.4 basic antibody-antigen docking tutorial**](/education/HADDOCK24/HADDOCK24-antibody-antigen-basic):
   This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information 
   about the hypervariable loops of the antibody and NMR data identifying the epitope.
   This tutorial does not require any Linux expertise and only makes use of our web servers and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
   The complex is also modelled using AlphaFold2 and the results compared to those obtained with HADDOCK.
 
+* [**HADDOCK2.4 basic protein-glycan tutorial**](/education/HADDOCK24/HADDOCK24-protein-glycan):
+  This tutorial explains the modelling of protein-glycan complexes using the HADDOCK2.4 webserver and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis. It is a basic, fully web-based tutorial requiring no Linux expertise.
+
+# Intermediate web server tutorials 
+
 * [**HADDOCK2.4 basic Protein-DNA tutorial**](/education/HADDOCK24/HADDOCK24-protein-DNA-basic):
   This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of a protein-DNA complex in which two protein units bind to the DNA in a symmetrical manner (3CRO). Next to ambiguous restraints to drive the docking symmetry restraints are defined to enforce symmetrical protein binding.
     This tutorial does not require any Linux expertise and only makes use of our web servers and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
@@ -43,6 +50,14 @@ In this page you can find links to tutorials on the usage of our software and we
   about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope.
   This tutorial does not require any Linux expertise and only makes use of our web servers and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
 
+* [**DISVIS/HADDOCK2.4 oligomer puzzle**](/education/HADDOCK24/XL-MS-oligomer):
+  In this tutorial you will have to solve an oligomer puzzle, namely predicting the correct oligomeric state
+  of a symmetrical homomer complex based on a few (artificial) cross-links.
+  The tutorial does not require any Linux expertise and only makes use of the DISVIS and HADDOCK web servers and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
+  It now also includes a part describing the modelling of these homomeric complexes using AlphaFold2.
+
+# Advanced web server tutorials 
+
 * [**HADDOCK2.4 ab-initio, multi-body symmetrical docking tutorial**](/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70):
   A tutorial demonstrating multi-body docking with HADDOCK using its ab-initio mode with symmetry restraints.
   It is based on a former CASP-CAPRI target (T70).
@@ -52,20 +67,25 @@ In this page you can find links to tutorials on the usage of our software and we
   It is an advanced tutorial requiring a Linux shell, which, next to using the HADDOCK2.4 webserver, also uses open-source chemoinformatics
   toolkits such as [RDKit](https://www.rdkit.org/){:target="_blank"}.
 
-* [**HADDOCK2.4 basic protein-glycan tutorial**](/education/HADDOCK24/HADDOCK24-protein-glycan):
-  This tutorial explains the modelling of protein-glycan complexes using the HADDOCK2.4 webserver and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis. It is a basic, fully web-based tutorial requiring no Linux expertise.
 
 * [**HADDOCK2.4 ligand binding site tutorial**](/education/HADDOCK24/HADDOCK24-binding-sites):
   A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites.
   The information from the ab-initio run is then used to setup a binding pocket-targeted protein-ligand docking run.
   We use as example the multidrug exporter AcrB.
 
-* [**DISVIS/HADDOCK2.4 oligomer puzzle**](/education/HADDOCK24/XL-MS-oligomer):
-  In this tutorial you will have to solve an oligomer puzzle, namely predicting the correct oligomeric state
-  of a symmetrical homomer complex based on a few (artificial) cross-links.
-  The tutorial does not require any Linux expertise and only makes use of the DISVIS and HADDOCK web servers and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis.
-  It now also includes a part describing the modelling of these homomeric complexes using AlphaFold2.
-
 * [**LightDock+HADDOCK membrane proteins tutorial**](/education/HADDOCK24/LightDock-membrane-proteins):
   This tutorial demonstrates the use of LightDock for predicting the structure of membrane receptor–soluble protein complex using the topological information 
   provided by the membrane to guide the modelling process. The resulting LightDock models are then refined using HADDOCK.
+
+# Documentation
+
+* [**HADDOCK best practice guide**](https://www.bonvinlab.org/software/bpg/){: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/new/haddock-restraints){:target="_blank"}.
+
+# HADDOCK2.4 local installation tutorial  
+
+* [**HADDOCK2.4 local installation tutorial**](/education/HADDOCK24/HADDOCK24-local-tutorial):
+  A tutorial demonstrating the installation and use of a local installation of HADDOCK2.4. It demonstrates various docking scenarios.
+  You will need for this a valid license of HADDOCK2.4.