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level. The simulated system is composed of the human TATA binding protein (TBP PDB: <a class="reference external" href="https://www.rcsb.org/structure/1c9b">1C9B</a>) bounded to the TATA box at the promoter region (-64 to +13) of the Human Immunodeficiency Virus type 1 (HIV-1, GenBank: <a class="reference external" href="https://www.ncbi.nlm.nih.gov/nuccore/K03455.1">K03455</a>, <strong>Figure 1</strong>). Solvent effects are considered implicitly using the Generalized Born model (GB).</p>
<p>The main references for this tutorial are: <a class="reference external" href="https://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c1cp21248f">Machado et al.</a> and <a class="reference external" href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">Machado &amp; Pantano</a>. We strongly advise you to read these articles before starting the tutorial.</p>
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<figcaption>
<p><span class="caption-text"><strong>Figure 1.</strong> Promoter region of HIV-1. The TATA box is highlighted in orange, while base pairs at 0.7nm of TBP are colored in yellow.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
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Expand Down Expand Up @@ -136,7 +134,8 @@ <h2>7.1.1. Embed the protein in a lipid bilayer<a class="headerlink" href="#embe
</div>
<p>Luckily, we already oriented the protein inside the membrane. For setting up your own system you can go to <a class="reference external" href="https://opm.phar.umich.edu/">Orientations of Proteins in Membranes (OPM) database</a> and (if your structure is available) use the dummy atoms provided there to make them match with your membrane model (see <strong>Figure 1</strong>).</p>
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<figcaption>
<p><span class="caption-text"><strong>Figure 1.</strong> Protein oriented inside the membrane from the OPM database with dummy atoms represented as orange spheres.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
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