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docked_single.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 Single 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>
<h3 id="currentPage">AMPs Docked to Single Biofilm Target</h3>
<a href="docked_dual.html"><h3>AMPs Docked to Dual Biofilm Targets</h3></a>
<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 100 AMPs, filtered from AMPs with known
anti-Gram positive activity, that have been evaluated for their ability to
interact with the active site triad (Cys-His-Arg) of the mutated
<a
target="_blank"
rel="noopener noreferrer"
style="color: white"
href="/all.html?pep=sortase"
>Class C Sortase protein</a
>
(in semi-open conformation) of <em>Corynebacterium striatum</em>. Based on
docking results, these AMPs have been grouped into 11 categories on a preference
scale of 0-10. This preference scale is based on interactions with the active
site residues, other important amino acid residues, as well as docking scores.
This is relevant in selecting candidate AMPs for future <em>in vitro</em> and
<em>in vivo</em>
studies that target sortase enzyme related processes. Each card for a particular
AMP contains its own input and output PDBQT files, model image and bond info,
which can be downloaded by clicking on the respective icons.
</p>
<br />
<p>
The Standard tab is the docking analysis of the LPMTG Motif of the Pilin Subunit
of <em>Corynebacterium striatum</em>.
</p>
<br />
<p>Protein-peptide docking studies were done using Autodock Vina.</p>
<br />
<a
style="color: white"
target="_blank"
data-goatcounter-title="(REDIRECT) Docking Interactions Reference Sheet"
href="static/pdf/reference_sheets/B-AMP_Docking_Interactions_ReferenceSheet.pdf"
>
Reference sheet for Docking Interactions
</a>
</section>
</div>
<div style="display: flex; justify-content: center">
<button id="toggleHelpButton" onclick="showHelpOverlay()">💡 SHOW HELP</button>
</div>
<section id="jumpListContainer">
<h1 style="margin-right: 10px; color: white">JUMP TO PREFERENCE SCORE</h1>
<ul id="jumpList"></ul>
</section>
<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>
<p>Color scheme for interacting residues within images.</p>
<section id="legends">
<span
class="legend"
style="background-image: linear-gradient(45deg, cornflowerblue, navy)"
>His168-Cys230-Arg239 Triad</span
>
<span
class="legend"
style="
background-image: linear-gradient(45deg, gold, orangered);
color: #353535;
"
>Other interacting residues</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_index.js"></script>
<script src="static/js/pep_to_activity_and_name_index.js"></script>
<script src="static/js/text_to_pep_index.js"></script>
<script src="static/js/docked_view.js"></script>
<script
data-goatcounter="https://b-amp.goatcounter.com/count"
async
src="//gc.zgo.at/count.js"
></script>
</body>
</html>