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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>Antimicrobial Peptide Repository for Biofilms | 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">
<h3 id="currentPage">Home</h3>
<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 Target</h3></a>
<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>
<section id="landing">
<section id="welcome">
<img src="static/images/AMPDB.svg" alt="logo" id="svgLogo" />
<h1>ANTIMICROBIAL PEPTIDE REPOSITORY FOR BIOFILMS</h1>
</section>
<section id="intro">
<p style="text-align: justify; text-justify: inter-word">
B-AMP v2.0 is a structural and functional repository consisting of
(i) 5766 AMPs from natural and synthetic sources, (ii) 2502 bacterial
protein targets from a wide-range of bacterial species, and (iii)
AMP-biofilm target models for well-known biofilm-forming pathogens.
B-AMP provides search enabled information for AMPs and biofilm targets,
that includes FASTA files, UniProt and PDB annotations, PDB and RoseTTAFold
structural models, and PubMed references to scientific literature. For the
3D AMP-protein docking models, PDBQT IN/OUT files, 3D models and bond
information is also provided. Taken together, B-AMP is a one-stop
bioinformatics resource for AMP investigations related to biofilms,
and can be leveraged for a range of studies across biofilm-forming
pathogens and potential biofilm targets.
</p>
</section>
</section>
<section id="paparazzi">
<h1>MEET THE TEAM</h1>
<section id="theTeam">
<section class="portraitContainer" id="gandhar">
<img src="static/portraits/gandhar.jpg" class="portrait" />
<h2 class="portraitLabel">Gandhar Tendulkar</h2>
<p class="affiliation">
M.Sc. Bioinformatics<br />
University of Mumbai, India
</p>
</section>
<section class="portraitContainer" id="maam">
<img src="static/portraits/karishma_maam.jpg" class="portrait" />
<h2 class="portraitLabel">Dr. Karishma S. Kaushik</h2>
<p class="affiliation">
Assistant Professor / Ramalingaswami Re-entry Fellow<br />
Savitribai Phule Pune University, India
</p>
</section>
<section class="portraitContainer" id="rohit">
<img src="static/portraits/rohit.jpg" class="portrait" />
<h2 class="portraitLabel">Rohit Awate</h2>
<p class="affiliation">
M.S. Computer Science<br />
Northeastern University, USA
</p>
</section>
<section class="portraitContainer" id="shreeya">
<img src="static/portraits/shreeya.jpg" class="portrait" />
<h2 class="portraitLabel">Shreeya Mhade</h2>
<p class="affiliation">
M.Sc. Bioinformatics<br />
University of Mumbai, India
</p>
</section>
<section class="portraitContainer" id="stutee">
<img src="static/portraits/stutee.jpg" class="portrait" />
<h2 class="portraitLabel">Stutee Panse</h2>
<p class="affiliation">
M.S. Biotechnology<br />
The Pennsylvania State University, USA<br />
</p>
</section>
<section class="portraitContainer" id="raghu_sir">
<img src="static/portraits/ragothaman_sir.jpg" class="portrait" />
<h2 class="portraitLabel">Dr. Ragothaman M Yennamalli</h2>
<p class="affiliation">
Assistant Professor<br />
SASTRA Deemed to be University, India<br />
</p>
</section>
<section class="portraitContainer" id="shashank">
<img src="static/portraits/shashank.jpg" class="portrait" />
<h2 class="portraitLabel">Shashank Ravichandran</h2>
<p class="affiliation">
B.Tech. Bioinformatics<br />
SASTRA Deemed to be University, India<br />
</p>
</section>
<section class="portraitContainer" id="yati">
<img src="static/portraits/yati.jpg" class="portrait" />
<h2 class="portraitLabel">Yatindrapravanan Narasimhan</h2>
<p class="affiliation">
B.Tech. Bioinformatics<br />
SASTRA Deemed to be University, India<br />
</p>
</section>
<section class="portraitContainer" id="supriya">
<img src="static/portraits/supriya.jpg" class="portrait" />
<h2 class="portraitLabel">Sai Supriya Avatapalli</h2>
<p class="affiliation">
Remote Internship<br />
Savitribai Phule Pune University, India<br />
</p>
</section>
</section>
</section>
<section id="citeUs">
<h1 style="font-size: 2.5em">HOW TO CITE US</h1>
<span class="citation" style="width: 80%">
<h4 class="citationInstruction">
Resources downloaded and/or used from B-AMP (as well as resources we have made
available on GitHub), including FASTA files, PDB files, 3D models, AMP lists,
code, should be cited with the link
<span style="display: inline-block; font-weight: bold; color: #555"
>b-amp.karishmakaushiklab.com</span
>, and the following citation:
</h4>
<h3 class="citationBody">
Mhade S, Panse S, Tendulkar G, Awate R, Narasimhan Y, Kadam S, Yennamalli RM and Kaushik KS (2021)
AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm
Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen.
Front. Cell. Infect. Microbiol. 11:803774. doi: <a target="_blank" href="https://doi.org/10.3389/fcimb.2021.803774">10.3389/fcimb.2021.803774</a>
</h3>
<h3 class="citationBody">
Ravichandran S, Avatapalli S, Narasimhan Y, Kaushik KS and Yennamalli RM (2022)
'Targeting' the search: An Upgraded Structural and Functional Repository of Antimicrobial
Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets.
Front. Cell. Infect. Microbiol. 12:1020391. doi: <a target="_blank" href="https://doi.org/10.3389/fcimb.2022.1020391">10.3389/fcimb.2022.1020391</a>
</h3>
</span>
</section>
<footer>
<img src="static/images/kaushik-lab-logo.png" id="labLogo" />
<section id="footerContent">
<p>A project by</p>
<h1>HUMAN-RELEVANT INFECTION BIOLOGY GROUP</h1>
<h2>(led by Dr. Karishma Kaushik)</h2>
<hr />
<section class="footerLinks">
<a
href="https://www.karishmakaushiklab.com/"
target="_blank"
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</a>
</section>
</section>
</footer>
<section id="license">
<p>
We will be updating this repository with additional AMP structures, Biofilm protein targets, and
protein-peptide docking models. Last update was on Aug 10, 2022.
</p>
<p>
While we have exercised multiple checks and continue to do so, B-AMP does not
guarantee that the resources are free of errors. Please use resources at your own
discretion and with verification.
</p>
<p>
This work is licensed under a
<a
rel="license"
style="color: white"
href="https://creativecommons.org/licenses/by/3.0/deed.en_US"
rel="noopener noreferrer"
target="_blank"
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>Creative Commons Attribution 3.0 Unported License</a
>, with the exception of this website's code and additional utility code that aided
this work, which is separately licensed under the
<a
rel="license"
style="color: white"
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/LICENSE"
rel="noopener noreferrer"
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub License GPLv3"
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</p>
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