From dd1a32562d03fac56fc3bac8f99800cc5a110856 Mon Sep 17 00:00:00 2001
From: Zhefu Li <zf-li23@mails.tsinghua.edu.cn>
Date: Tue, 1 Oct 2024 08:18:02 +0000
Subject: [PATCH] Update model.html
---
wiki/pages/model.html | 25 ++++++++++++++++++++++++-
1 file changed, 24 insertions(+), 1 deletion(-)
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 278daf80..99b5781f 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -458,7 +458,6 @@
<h2 id="topic2">
<h2>Molecular Dynamics Simulations of Muscone with its Receptor</h2>
<hr>
- <h2>Molecular Dynamics Simulations of Muscone with its Receptor</h2>
<p>One of the major contributions of our project was the development of a signaling pathway activated by
gas molecules acting as switches, so we were interested in the behavior of the muscone when bound to
its receptor. Molecular dynamics simulations can help us to visualize the binding process, track the
@@ -470,6 +469,30 @@
prepare the three-dimensional molecular model of the research object. In this study, our goal is
to simulate the interaction between muscone and the olfactory receptor Or5an6 (MOR215-1).</li>
</ul>
+ <h4>1. Constructing the Three-Dimensional Structures of Muscone and the Receptor:</h4>
+
+ <ul>
+ <li><strong>Muscone</strong>:</li>
+ <ul>
+ <li>Obtain the molecular structure information of muscone from the PubChem database. PubChem is
+ a widely used chemical information database that provides data on molecular structures,
+ chemical properties, and biological activities.</li>
+ <li>Molecular structure obtained from PubChem <a
+ href="https://pubchem.ncbi.nlm.nih.gov/compound/10947">link</a></li>
+ </ul>
+ <div class="image-container">
+ <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/3-methylcyclopentadecanone.png"
+ alt="Muscone" class="shadowed-image" style="width: 50%; max-width: 500px;">
+ </div>
+ <ul>
+ <li>Next, use the chemical modeling tool Avogadro to convert this structure into a PDB format
+ file (<code>muscone.pdb</code>) for further simulation and analysis. This step ensures that
+ the three-dimensional geometric structure of muscone is accurate and suitable for subsequent
+ molecular docking and dynamics simulations.</li>
+ <li>Avogadro converts to pdb format <code>muscone.pdb</code></li>
+ <li><img src="muscone.png" alt="Muscone"></li>
+ </ul>
+ </ul>
</div>
</div>
--
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