From 4b86225e8cbbb26c497ebc70cfddaca0c7abcb15 Mon Sep 17 00:00:00 2001
From: Zhefu Li <zf-li23@mails.tsinghua.edu.cn>
Date: Tue, 1 Oct 2024 12:01:57 +0000
Subject: [PATCH] Update model.html
---
wiki/pages/model.html | 66 +++++++++++++++++++++++++++++++++++++++++--
1 file changed, 63 insertions(+), 3 deletions(-)
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 2db59995..4d9673db 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -789,7 +789,7 @@
dit xvg_show -f temperature.xvg
</code></pre>
<div class="image-container">
- <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/3-pressure.png" alt="pressure"
+ <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/pressure.png" alt="pressure"
class="shadowed-image" style="width: 50%; max-width: 500px;">
</div>
<p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 9 Curve of the pressure over time
@@ -924,13 +924,73 @@
of the results.</li>
</ul>
<div class="image-container">
- <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/rmsd.png" alt="RMSD"
+ <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/rmsd.png" alt="RMSD Plot"
class="shadowed-image" style="width: 50%; max-width: 500px;">
</div>
<p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 14 RMSD Analysis
</p>
+ <h4>3. Radius of Gyration (Rg) Calculation</h4>
- <img src="rmsd.png" alt="RMSD Plot">
+ <ul>
+ <li>The radius of gyration (Rg) is used to assess the compactness of a protein and is an important
+ indicator of protein folding or unfolding.</li>
+ <li>If the protein folding is stable, its radius of gyration Rg will maintain a relatively stable
+ value. If the protein unfolds, its Rg will change over time.</li>
+ </ul>
+
+ <pre><code>gmx gyrate -s md_0_10.tpr -f md_0_10_fit.xtc -o gyrate.xvg
+ #1
+ xmgrace gyrate.xvg
+ </code></pre>
+
+ <ul>
+ <li>In the simulation, the Rg value of the protein remained between 2.2 and 2.25 nanometers,
+ indicating that the protein maintained a compact folded state during the simulation period at
+ 300 K, with no significant unfolding or expansion occurring.</li>
+ </ul>
+ <div class="image-container">
+ <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/gr1.png"
+ alt="Additional Radius of Gyration Plot" class="shadowed-image"
+ style="width: 50%; max-width: 500px;">
+ </div>
+ <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 15 Radius of Gyration Calculation
+ </p>
+ <h4>4. Protein-Ligand Interaction Energy</h4>
+
+ <ul>
+ <li>By calculating the Coulomb and Lennard-Jones interaction energies within the system, the binding
+ energy between musk ketone and the receptor is quantified.</li>
+ </ul>
+
+ <pre><code>gmx make_ndx -f em.gro -o index.ndx
+ > 1 | 13
+ gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
+ gmx mdrun -deffnm ie -rerun md_0_10.xtc -nb cpu
+
+ gmx energy -f ie.edr -o interaction_energy.xvg
+
+ Energy Average Err.Est. RMSD Tot-Drift
+ -------------------------------------------------------------------------------
+ Coul-SR:Protein-MUS 0.0439222 0.38 2.88794 1.41131 (kJ/mol)
+ LJ-SR:Protein-MUS -81.3724 1.6 9.75743 1.99715 (kJ/mol)
+ #21 | 22
+
+ xmgrace interaction_energy.xvg
+ dit xvg_show -f interaction_energy.xvg
+ </code></pre>
+ <div class="image-container">
+ <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/energy.png"
+ alt="Interaction Energy Plot" class="shadowed-image" style="width: 50%; max-width: 500px;">
+ </div>
+ <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 16 Protein-Ligand Interaction
+ Energy
+ </p>
+
+ <ul>
+ <li>The calculation results show that the Lennard-Jones interaction dominates in stable binding,
+ averaging -81.37 kJ/mol, indicating that hydrophobic interactions play a central role in the
+ binding between the ligand and the receptor.</li>
+ </ul>
</div>
</div>
--
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