diff --git a/ippisite/ippidb/templates/targetcentric.html b/ippisite/ippidb/templates/targetcentric.html
index 6f5ffb20fc93c62c999ed9fdd51328bca0c5b4c9..81e1126fdc7531add4c47f27ef131c5a59b50855 100644
--- a/ippisite/ippidb/templates/targetcentric.html
+++ b/ippisite/ippidb/templates/targetcentric.html
@@ -177,17 +177,14 @@
<div class="mb-3 card {% if forloop.counter == 1 %} border-primary {% else %} border-info {% endif %} border_card"
id="card_{{ forloop.counter }}">
<div class="card-header text-center">
- <a class="submithref" href="{% url 'cavities' %}?pdbsearch={{ pdb.code }}"><strong>{{
- pdb.code }}</strong></a>
+ <a class="submithref" href="{% url 'cavities' %}?pdbsearch={{ pdb.code }}"><strong>{{ pdb.code }}</strong></a>
</div>
<div class="card-body text-nowrap">
{% for chain in pdb.chain_set.all %}
Chain {{ chain.pdb_chain_id }} <a class="submithref"
- href="{% url 'cavities' %}?uniprotid={{ chain.protein.uniprot_id }}">{{
- chain.protein.uniprot_id }}</a>
+ href="{% url 'cavities' %}?uniprotid={{ chain.protein.uniprot_id }}">{{ chain.protein.uniprot_id }}</a>
<a class="submithref"
- href="{% url 'cavities' %}?organism={{ chain.protein.organism.name }}">{{
- chain.protein.organism.name }}</a>
+ href="{% url 'cavities' %}?organism={{ chain.protein.organism.name }}">{{ chain.protein.organism.name }}</a>
</br>
{% endfor %}
</div>
@@ -266,8 +263,7 @@ Comparison and druggability prediction of protein-ligand binding sites from phar
<tr>
{% for td in avg_std|make_list %}
{% if forloop.first %}
- <td style="background-color:rgb({{ td|get_color }})" title="{{ td }}">{{
- td|floatformat:2|intcomma }}</td>
+ <td style="background-color:rgb({{ td|get_color }})" title="{{ td }}">{{ td|floatformat:2|intcomma }}</td>
{% elif forloop.last %}
<td style="direction: rtl;background-color:rgb({{ td|get_color }})"
title="{{ td }}">{{ td|floatformat:2|intcomma }}</td>
diff --git a/ippisite/ippidb/templates/tutorials.html b/ippisite/ippidb/templates/tutorials.html
index bd4de8bd2a62120b7de9e9082dd0bdc10891e18f..881134343fb41a6d68f5e2001b37e319a5837a5d 100644
--- a/ippisite/ippidb/templates/tutorials.html
+++ b/ippisite/ippidb/templates/tutorials.html
@@ -49,7 +49,20 @@
allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe>
<div class="card-body">
- <p class="card-text">Visualize pockets on the Protein Interaction Explorer.</p>
+ <p class="card-text">
+ This tutorial guides the user on how to:
+ <ul>
+ <li>navigate and
+ access the Protein Interaction Explorer (PIE) section of the IPPIDB
+ web-server</li>
+ <li>view list of PIE functionalities</li>
+ <li>display all available pockets in PIE as an “Overview†list</li>
+ <li>search for any protein they want to visualize</li>
+ <li>open the PIE 3D viewer to display the protein chains and associated
+ pockets</li>
+ <li>move/zoom 3D structures on the viewer</li>
+ </ul>
+ </p>
</div>
</div>
</div>
@@ -68,7 +81,7 @@
<p class="card-text">A short video that shows how you can efficiently add new
data
- to iPPI-DB using the contribute mode and your ORCID ID</p>
+ to iPPI-DB using the contribute mode and your ORCID ID.</p>
</div>
</div>
</div>
@@ -84,8 +97,26 @@
allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe>
<div class="card-body">
- <p class="card-text">Analyze druggability / interactibility of proteins on the
- Protein Interaction Explorer.</p>
+ <p class="card-text">This tutorial shows how to use the PIE (Protein Interaction
+ Explorer) 3D viewer to:
+ <ul>
+ <li>display and scale druggability prediction scores by InDeep<sup>*</sup>
+ <strong>and superpose them on the 3D protein
+ structures
+ </li>
+ <li>display and
+ scale InDeep<sup>*</sup></strong>predicted interactibility scores
+ superposed on 3D protein
+ structures</li>
+ </ul>
+ </p>
+ <p class="card-text"><sup>*</sup><small>Indeep: V. Mallet, L. Ruano, A. Franel,
+ M. Nilges, K.
+ Druart,
+ G.Bouvier, O.Sperandio, InDeep: 3D fully convolutional neural networks
+ to assist in silico drug design on protein-protein interactions,
+ Bioinformatics, Volume 38, Issue 5, March 2022, Pages 1261-1268</small>
+ </p>
</div>
</div>
</div>
@@ -106,8 +137,15 @@
allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe>
<div class="card-body">
- <p class="card-text">Visualize hotspots and ligands on the Protein Interaction
- Explorer.</p>
+ <p class="card-text">This tutorial shows how to use the PIE (Protein Interaction
+ Explorer) 3D viewer to:
+ <ul>
+ <li>visualize hotspots detected by FoldX for a protein complex</li>
+ <li>visualize ligands superposed with chains of related
+ proteins</li>
+ <li>show colocalization of ligands with predicted hot spots</li>
+ </ul>
+ </p>
</div>
</div>
</div>
@@ -128,8 +166,17 @@
allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe>
<div class="card-body">
- <p class="card-text">Study closely related pockets on the Protein Interaction
- Explorer.</p>
+ <p class="card-text">This tutorial shows how one can:
+ <ul>
+ <li>explore the “Pockets†section of the PIE</li>
+ <li>for a given pocket on a displayed protein, display list of all similar
+ pockets from the iPPI-DB database</li>
+ <li>display PSI metric (Pocket Similarity Index) for all the pockets with
+ respect to the given pocket</li>
+ <li>display list of physio-chemical descriptors for all the “similarâ€
+ pockets</li>
+ </ul>
+ </p>
</div>
</div>
</div>
@@ -149,7 +196,19 @@
allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe>
<div class="card-body">
- <p class="card-text">How to use the TMAP on the Protein Interaction Explorer.
+ <p class="card-text">
+ This tutorial shows how to:
+ <ul>
+ <li>access and use the TMAP
+ (pocketome) feature of PIE (Protein Interaction Explorer)</li>
+ <li>Use the “Chart Help†feature to learn how to navigate the TMAP</li>
+ <li>meaning of different criteria or legends which can be viewed on TMAP
+ </li>
+ <li>color code TMAP with different criteria</li>
+ <li>search and query information for a complex via TMAP window</li>
+ <li>format the names of HD (heterodimer) and PL (protein-ligand) pockets
+ </li>
+ </ul>
</p>
</div>
</div>