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Commit 44a88529 authored by Cheng Wui Lim's avatar Cheng Wui Lim
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<p>The interactions between Methylene Blue and Proteins of interest are analyzed by Discovery Studio (BIOVIA DS, 2016), and visualized by PyMOL (Schrodinger LLC, 2020). Note that MB has different binding sites among all proteins of interest.</p>
<p>The above analysis serves as preliminary models to identify and visualize interactions between Methylene Blue and Proteins of interest.</p>
<p></p>
<h5 style="text-align center">2BOQ: <i>Pleurotus eryngii</i> Versatile Peroxidase (vpl2)</h5>
<h5>2BOQ: <i>Pleurotus eryngii</i> Versatile Peroxidase (vpl2)</h5>
<figure style="text-align:center;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/2boq-2d.jpeg" style="max-width: 600px;max-height: 600px;">
</figure>
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<iframe title="PLKNPLC-HK: 2boq VMD video (2023) [English]" width="560" height="315" src="https://video.igem.org/videos/embed/c987198a-9ab4-4b5d-bd34-16cc57c59f61" frameborder="0" allowfullscreen="" sandbox="allow-same-origin allow-scripts allow-popups"></iframe>
</figure>
<p></p>
<h5 style="text-align center">3M5Q: <i>Phanerodontia chrysosporium</i> Magnesium Peroxidase (mnp1)</h5>
<h5>3M5Q: <i>Phanerodontia chrysosporium</i> Magnesium Peroxidase (mnp1)</h5>
<figure style="text-align:center;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/3m5q-2d.jpeg" style="max-width: 600px;max-height: 600px;">
</figure>
......@@ -117,7 +117,7 @@
<iframe title="PLKNPLC-HK: 3m5q VMD video (2023) [English]" width="560" height="315" src="https://video.igem.org/videos/embed/61758bda-ad12-407a-8d88-f35974eeabcc" frameborder="0" allowfullscreen="" sandbox="allow-same-origin allow-scripts allow-popups"></iframe>
</figure>
<p></p>
<h5 style="text-align center">1KYA: Trametes versicolor Laccase (lac2)</h5>
<h5>1KYA: Trametes versicolor Laccase (lac2)</h5>
<figure style="text-align:center;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/1kya-2d.jpeg" style="max-width: 600px;max-height: 600px;">
</figure>
......@@ -129,7 +129,7 @@
<iframe title="PLKNPLC-HK: 1KYA VMD video (2023) [English]" width="560" height="315" src="https://video.igem.org/videos/embed/ce34848b-9cab-42ff-847f-8b8979a3583d" frameborder="0" allowfullscreen="" sandbox="allow-same-origin allow-scripts allow-popups"></iframe>
</figure>
<p></p>
<h5 style="text-align center">1B80: <i>Phanerodotia chrysosporium</i> Lignin Peroxidase H8 (liph8)</h5>
<h5>1B80: <i>Phanerodotia chrysosporium</i> Lignin Peroxidase H8 (liph8)</h5>
<figure style="text-align:center;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/1b80-2d.jpeg" style="max-width: 600px;max-height: 600px;">
</figure>
......@@ -141,7 +141,7 @@
<iframe title="PLKNPLC-HK: 1b80 VMD video (2023) [English]" width="560" height="315" src="https://video.igem.org/videos/embed/274de8fd-19e1-4426-8726-4d7f9ec5f57e" frameborder="0" allowfullscreen="" sandbox="allow-same-origin allow-scripts allow-popups"></iframe>
</figure>
<p></p>
<h5 style="text-align center">TvLiP: <i>Trametes versicolor</i> Lignin Peroxidase (lpg3)</h5>
<h5>TvLiP: <i>Trametes versicolor</i> Lignin Peroxidase (lpg3)</h5>
<figure style="text-align:center;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/tvlip-2d.png" style="max-width: 600px;max-height: 600px;">
</figure>
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</div>
<div class="col-lg-12">
<h5 style="text-align center">The SwissDock binding mode cluster with lowest FullFitness Energetics is shown below</h5>
<h5>The SwissDock binding mode cluster with lowest FullFitness Energetics is shown below</h5>
<figure style="text-align:center;">
<figcaption>2BOQ: Pleurotus eryngii Versatile Peroxidase (vpl2)</figcaption>
<img src="https://static.igem.wiki/teams/4936/wiki/results/2boq-energetics-2.png" style="max-width: 600px;max-height: 600px;">
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<div class="col-lg-12">
<hr>
<h5 style="text-align center">Reference:</h5>
<h5>Reference:</h5>
<ul>[1] Grosdidier, A., Zoete, V., & Michielin, O. (2007). EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins, 67(4), 1010–1025. https://doi.org/10.1002/prot.21367</ul>
<ul>[2] Hekkelman, M. L., De Vries, I., Joosten, R. P., & Perrakis, A. (2022). AlphaFill: enriching AlphaFold models with ligands and cofactors. Nature Methods, 20(2), 205–213. https://doi.org/10.1038/s41592-022-01685-y</ul>
<ul>[3] Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Овчинников, С. Г., & Steinegger, M. (2022). ColabFold: making protein folding accessible to all. Nature Methods, 19(6), 679–682. https://doi.org/10.1038/s41592-022-01488-1</ul>
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