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docked_dual.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>AMPs Docked to Dual Biofilm Target | B-AMP</title>
<link rel="icon" type="image/x-icon" href="./static/images/favicon.ico">
<link rel="stylesheet" href="static/css/style.css" />
</head>
<body>
<nav>
<h1 id="siteTitle">B-AMP</h1>
<section id="navLinksSection">
<a href="index.html"><h3>Home</h3></a>
<a href="all.html"><h3>AMP Library</h3></a>
<a href="anti_gram_positive.html"><h3>Anti Gram Positive AMPs</h3></a>
<a href="anti_gram_negative.html"><h3>Anti Gram Negative AMPs</h3></a>
<a href="targets.html"><h3>Biofilm Targets</h3></a>
<a href="docked_single.html"><h3>AMPs Docked to Single Biofilm Targets</h3></a>
<h3 id="currentPage">AMPs Docked to Dual Biofilm Targets</h3>
<a href="code.html"><h3>Code</h3></a>
<a href="references.html"><h3>References</h3></a>
</section>
</nav>
<div class="bubbleWrap">
<section class="helpBubble">
<p>
This section consists of a library of 25 AMPs, filtered from AMPs with both
anti-Gram positive and anti-Gram negative activity, that have been evaluated
for their ability to interact with the active site regions of Target 1 or the
‘biofilm-associated surface protein’ of <i>Staphylococcus aureus</i> and Target 37 or
the ‘fimbrial subunit CupB6’ of <i>Pseudomonas aeruginosa</i>. Based on negative energy
binding scores and binding energy differences in the range of ± 1 kcal/mol, AMPs
were filtered to present a list of candidate AMPs for both biofilm targets. Based
on the proposed candidate list, AMPs can be taken up for further in silico evaluation
such as AMP-biofilm target dynamic interactions and MD simulations, as well as <i>in
vitro</i> and <i>in vivo</i> evaluation against mixed-species <i>P. aeruginosa</i> and <i>S. aureus</i> biofilms.
Each card for a particular AMP contains PDBQT and docking files, and model image which
can be downloaded by clicking on the respective icons.
</p>
<br />
<p>Protein-peptide docking studies were done using Autodock 4.2.</p>
<br />
<a
style="color: white"
target="_blank"
data-goatcounter-title="(REDIRECT) Docking Interactions Reference Sheet"
href="static/pdf/reference_sheets/B-AMP_Dual_Docking_ReferenceSheet.pdf"
>
Reference sheet for Dual Target Docking analysis
</a>
</section>
</div>
<div style="display: flex; justify-content: center">
<button id="toggleHelpButton" onclick="showHelpOverlay()">💡 SHOW HELP</button>
</div>
<main id="drampCards" style="margin-bottom: 100px"></main>
<section id="helpOverlay" class="overlay">
<div style="display: flex; justify-content: flex-end; width: 95%">
<img
src="static/icons/close.png"
alt="close-icon"
width="32"
onclick="hideHelpOverlay()"
id="closeHelpButton"
/>
</div>
<h1>LEGEND</h1>
<p>
Each card in the search results is color-coded as per the activity exhibited by that
peptide.
</p>
<section id="legends">
<span class="legend antiGramPositive">Anti-Gram Positive</span>
<span class="legend antiGramNegative">Anti-Gram Negative</span>
<span class="legend bothActivities">Anti-Gram Positive & Negative</span>
<span class="legend otherActivity">
Other Activity <br />
<p style="font-size: 0.7em">(Non anti-bacterial)</p>
</span>
</section>
</section>
<script src="static/js/pep_to_dramp_index.js"></script>
<script src="static/js/dramp_to_pep_index.js"></script>
<script src="static/js/pep_to_docking_score_dual_index.js"></script>
<script src="static/js/pep_to_activity_and_name_index.js"></script>
<script src="static/js/docked_dual_view.js"></script>
<script
data-goatcounter="https://b-amp.goatcounter.com/count"
async
src="//gc.zgo.at/count.js"
></script>
</body>
</html>