reusable tutorial sections concept

education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-BioExcel2024

@@ -30,7 +30,7 @@ needs to be highly variable to be able to bind to antigens of various nature (hi
 In this tutorial, we will concentrate on the terminal **variable domain (Fv)** of the Fab region.
 
 <figure style="text-align: center;">
-  <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/antibody_described.png">
+  <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/antibody_described.png">
 </figure>
 
 The small part of the Fab region that binds the antigen is called **paratope**. The part of the antigen
@@ -39,7 +39,7 @@ known as **complementarity-determining regions (CDRs)** or hypervariable loops w
 and conformation are altered to bind to different antigens. CDRs are shown in red in the figure below:
 
 <figure style="text-align: center;">
-  <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/CDRs.png">
+  <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/CDRs.png">
 </figure>
 
 In this tutorial we will be working with Interleukin-1β (IL-1β)
@@ -98,7 +98,7 @@ parameterisable yet rigid simulation pipeline composed of three steps:
 `rigid-body docking (it0)`, `semi-flexible refinement (it1)`, and `final refinement (itw)`.
 
 <figure style="text-align: center;">
-<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/HADDOCK2-stages.png">
+<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/HADDOCK2-stages.png">
 </figure>
 
 In HADDOCK3, users have the freedom to configure docking workflows into
@@ -119,7 +119,7 @@ restraints can, however, be used in HADDOCK3, which also supports the
 *ab initio* docking modes of HADDOCK.
 
 <figure style="text-align: center;">
-<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/HADDOCK3-workflow-scheme.png">
+<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/HADDOCK3-workflow-scheme.png">
 </figure>
 
 To keep HADDOCK3 modules organized, we catalogued them into several
@@ -519,7 +519,7 @@ Do the identified paratope residues form a well-defined patch on the surface?
     <b><i>See surface view of the paratope</i></b> <i class="material-icons">expand_more</i>
   </summary>
   <figure style="text-align: center;">
-    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/antibody-paratope.png">
+    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/antibody-paratope.png">
   </figure>
   <br>
 </details>
@@ -533,7 +533,7 @@ to map the binding site of the antibody (gevokizumab) on Interleukin-1β.
 The residues affected by binding are listed in Table 5 of [Blech et al. JMB 2013](https://dx.doi.org/10.1016/j.jmb.2012.09.021){:target="_blank"}:
 
 <figure style="text-align: center;">
-  <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/Table5-Blech.png">
+  <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/Table5-Blech.png">
 </figure>
 
 The list of binding site (epitope) residues identified by NMR is:
@@ -569,7 +569,7 @@ The answer to that question should be yes, but we can see some residues not colo
     <b><i>See surface view of the epitope identified by NMR</i></b> <i class="material-icons">expand_more</i>
   </summary>
   <figure style="text-align: center;">
-    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/antigen-epitope.png">
+    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/antigen-epitope.png">
   </figure>
   <br>
 </details>
@@ -611,7 +611,7 @@ color green, passive<br>
     <b><i>See the epitope and passive residues</i></b> <i class="material-icons">expand_more</i>
   </summary>
   <figure style="text-align: center;">
-    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/antigen-active-passive.png">
+    <img width="60%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/antigen-active-passive.png">
   </figure>
   <br>
 </details>
@@ -1298,7 +1298,7 @@ Simply click on the arrows of the term you want to use to sort the table (and yo
 A snapshot of this table is shown below:
 
 <figure style="text-align: center;">
-    <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/caprieval_analysis-table.png">
+    <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/caprieval_analysis-table.png">
 </figure>
 
 You can also view this report online [here](plots/report.html){:target="_blank"}
@@ -1333,7 +1333,7 @@ These are interactive plots. A menu on the top right of the first row (you might
 allows you to zoom in and out in the plots and turn on and off clusters. 
 
 <figure style="text-align: center;">
-    <img width="100%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/caprieval_analysis-plots.png">
+    <img width="100%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/caprieval_analysis-plots.png">
 </figure>
 
 As a reminder, you can also view this report online [here](plots/report.html){:target="_blank"}
@@ -1346,7 +1346,7 @@ Examine the plots (remember here that higher DockQ values and lower i-RMSD value
 Finally, the report also shows plots of the cluster statistics (distributions of values per cluster ordered according to their HADDOCK rank):
 
 <figure style="text-align: center;">
-    <img width="100%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/caprieval_analysis-distributions.png">
+    <img width="100%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/caprieval_analysis-distributions.png">
 </figure>
 
 <a class="prompt prompt-question">For this antibody-antigen case, which of the score components correlates best with the quality of the models?</a>
@@ -1520,7 +1520,7 @@ Are the residues of the paratope and NMR epitope at the interface?
  </summary>
  <p> Top-ranked model of the top cluster (cluster1_model_1) superimposed onto the reference crystal structure (in yellow)</p>
  <figure style="text-align: center">
-   <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/results-best-model.png">
+   <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/results-best-model.png">
  </figure>
  <br>
 </details>
@@ -1568,7 +1568,7 @@ How many interface clusters were found for this protein?
 Once you download the output archive, you can find the clustering information presented in the dendrogram:
 
 <figure style="text-align: center;">
-<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/dendrogram_average_P01584.png">
+<img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/dendrogram_average_P01584.png">
 </figure>
 
 We can see how the two *4G6M* antibody chains are recognized as a unique cluster, clearly separated from the other binding surfaces and, in particular, from those proper to IL-1RI (uniprot ID P14778).
@@ -2164,7 +2164,7 @@ Our antibody-antigen complex consists of three interfaces:
   <br>
   </summary>
   <figure align="center">
-   <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/abagtest_2d03e_pae.png">
+   <img src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/abagtest_2d03e_pae.png">
   </figure>
 </details>
 <br>
@@ -2240,7 +2240,7 @@ Does any model have the NMR-identified epitope at the interface with the antibod
   <br>
   </summary>
   <figure align="center">
-   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/ab-ag-af2.png">
+   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/ab-ag-af2.png">
   </figure>
   <br>
 </details>
@@ -2266,7 +2266,7 @@ alignto sele
   <br>
   </summary>
   <figure align="center">
-   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/ab-ag-af2-4G6M.png">
+   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/ab-ag-af2-4G6M.png">
   </figure>
   <br>
 </details>
@@ -2288,7 +2288,7 @@ Try to reproduce the previous steps and examine the quality of the various gener
   <br>
   </summary>
   <figure align="center">
-   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/ab-ag-af3-epitope.png">
+   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/ab-ag-af3-epitope.png">
   </figure>
   <br>
 </details>
@@ -2301,7 +2301,7 @@ Try to reproduce the previous steps and examine the quality of the various gener
   <br>
   </summary>
   <figure align="center">
-   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/ab-ag-af3-4G6M.png">
+   <img width="90%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/ab-ag-af3-4G6M.png">
   </figure>
   <br>
 </details>
@@ -2369,7 +2369,7 @@ You will land on the workflow-builder page, where you can interactively build yo
 This page is subdivided into three areas described below.
 
 <figure style="text-align: center;">
-  <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/haddock3-webapp-workflow-builder.png">
+  <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/haddock3-webapp-workflow-builder.png">
 </figure>
 
 On the left is presented the list of modules.
@@ -2424,7 +2424,7 @@ On the right side of the table, actions can be performed.
 The current implementation allows to rename a run or to delete it.
 
 <figure style="text-align: center;">
-  <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/haddock3-webapp-manage-run-access.png">
+  <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/haddock3-webapp-manage-run-access.png">
 </figure>
 
 To access the content of a run, click on its name to be directed to the haddock3 webapp results page.

education/HADDOCK3/HADDOCK3-antibody-antigen/sections/analysis-clusters.md

@@ -0,0 +1,34 @@
+### Cluster statistics
+
+Let us now analyse the docking results. Use for that either your own run or a pre-calculated run provided in the `runs` directory.
+Go into the `analysis/10_caprieval_analysis` directory of the respective run directory  (if needed copy the run or that directory to your local computer) and open in a web browser the `report.html` file. Be patient as this page contains interactive plots that may take some time to generate.
+
+On the top of the page, you will see a table that summarises the cluster statistics (taken from the `capri_clt.tsv` file).
+The columns (corresponding to the various clusters) are sorted by default on the cluster rank, which is based on the HADDOCK score (found on the 4th row of the table).
+As this is an interactive table, you can sort it as you wish by using the arrows present in the first column.
+Simply click on the arrows of the term you want to use to sort the table (and you can sort it in ascending or descending order).
+A snapshot of this table is shown below:
+
+<figure style="text-align: center;">
+    <img width="75%" src="/education/HADDOCK3/HADDOCK3-antibody-antigen/images/caprieval_analysis-table.png">
+</figure>
+
+You can also view this report online [here](plots/report.html){:target="_blank"}
+
+*__Note__* that in case the PDB files are still compressed (gzipped) the download links will not work. Also online visualisation is not enabled. To overcome this disk space storge solution, consider adding the global parameter `clean = true` at the begining of your configuration file.
+
+
+<a class="prompt prompt-info">Inspect the final cluster statistics</a>
+
+<a class="prompt prompt-question">How many clusters have been generated?</a>
+
+<a class="prompt prompt-question">Look at the score of the first few clusters: Are they significantly different if you consider their average scores and standard deviations?</a>
+
+Since for this tutorial we have at hand the crystal structure of the complex, we provided it as reference to the `caprieval` modules.
+This means that the iRMSD, lRMSD, Fnat and DockQ statistics report on the quality of the docked model compared to the reference crystal structure.
+
+<a class="prompt prompt-question">How many clusters of acceptable or better quality have been generate according to CAPRI criteria?</a>
+
+<a class="prompt prompt-question">What is the rank of the best cluster generated?</a>
+
+<a class="prompt prompt-question">What is the rank of the first acceptable of better cluster generated?</a>

education/HADDOCK3/HADDOCK3-antibody-antigen/sections/analysis-contacts.md

@@ -0,0 +1,16 @@
+### Contacts analysis
+
+We have recently added a new contact analysis module to HADDOCK3 that generates for each cluster both a contact matrix of the entire system showing all contacts within a 4.5Å cutoff and a chord chart representation of intermolecular contacts.
+
+In the current workflow we run, those files can be found in the `11_contactmap` directory.
+These are again html files with interactive plots (hover with your mouse over the plots).
+
+<a class="prompt prompt-info">
+Open in your favorite web browser the _cluster1_contmap_chordchart.html_ file to analyse the intermolecular contacts of the best-ranked cluster.
+</a>
+
+This file taken from the pre-computed run can also directly be visualized [here](cluster1_contmap_chordchart.html){:target="_blank"}
+
+<a class="prompt prompt-question">
+Can you identify which residue(s) make(s) the most intermolecular contacts?
+</a>