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Commit 54ee9a2f authored by Fabien MAREUIL's avatar Fabien MAREUIL
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add tutorials texts

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ippisite/ippidb/templates/targetcentric.html
+ 4
− 8
View file @ 54ee9a2f
......@@ -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>
......
ippisite/ippidb/templates/tutorials.html
+ 68
− 9
View file @ 54ee9a2f
......@@ -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 “similar”
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>
......
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