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<!DOCTYPE html>
<html>
<body>
<h1>PACMANS</h1>
<h2>Protease-ase Cleavages from MEROPS Analyzed Specificities</h2>
<img src="ProteaseAseSchematic.jpg" alt="Protease-ase Schematic" style="width:534px;height:360px;">
<br><br>
<div class="panel-body">
<p> This work has been published by <a href="http://onlinelibrary.wiley.com/doi/10.1002/pro.3113/abstract" target="_blank">Ferrall-Fairbanks et al in Protein Science.</a><p>
<h3>Usage Instructions:</h3>
<ol>
<li>
Choose a Protease-ase name and substrate name. These names are used to name the output file.
</li>
<li>[Optional] Choose a pocket size. Defaults are 1-8.</li>
<li>Navigate to <a href="http://merops.sanger.ac.uk/" target="_blank">MEROPS</a> and choose a protease-ase that has a specificity matrix and copy the link to that page. </li>
<p style="margin-left:2%; margin-right:2%;">As an example, find the link to the specificity matrix of cathepsin S: <font color="blue">https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=C01.034;type=P</font></p>
<li>Enter the amino acid sequence of the substrate. This sequence must be in FASTA format without any spaces.</li>
<li> These sequences can be obtained from <a href="http://www.uniprot.org/" target="_blank">Uniprot</a> or <a href="https://www.ncbi.nlm.nih.gov/protein/" target="_blank"> Pubmed Protein </a>. </li>
<p style="margin-left:2%; margin-right:2%;"> As an example to test, use the sequence for cathepsin K: <font color="blue"> <br>
MWGLKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMN <Br>
HLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQL <br>
KKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIP <br>
EGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGN <Br>
KGYILMARNKNNACGIANLASFPKM</font></p>
<li> Copy and paste your selected sequence or this example sequence into the indicated text box below </li>
</ol>
<p></p>
<p></p>
</div>
<form action="analyze.php" method="get" autocomplete="on">
<fieldset>
<legend><p style="font-size:140%;"><b>Protease-ase</b></p></legend>
Name:<br>
<input type="text" name="proase" placeholder="ex: catS" required><br>
MEROPS link:<br>
<input type="url" name="url" placeholder="httpp://merops.sanger.ac.uk/url" size="50" required>
</fieldset>
<br>
<fieldset>
<legend><p style="font-size:140%;"><b>Substrate Protease</b></p></legend>
Name:<br>
<input type="text" name="subpro" placeholder="ex: catK" required><br>
Amino acid sequence:<br>
<input type="text" name="sequence" placeholder="AAAAAAAA" size="100" required>
</fieldset>
<!--
<br>
<fieldset>
<legend><p style="font-size:140%;"><b>Pocket Size</b></p></legend>
This feature allows users to select a smaller subsection and look at the specificity of the active site pocket and its nearest neighbors only. The S4 on the protease-ase in the diagram corresponds to a bound of 1 and S4' corresponds to a bound of 8. Pocket size must be between 2 and 8.<br><br>
Lower bound:<br>
<input type="number" name="startp" min="1" max="7" step="1" value="1" size="4" required><br>
Upper bound:<br>
<input type="number" name="endp" min="2" max="8" step="1" value="8" size="4" required><br>
</fieldset>
-->
<br>
<input type="submit" value="Submit" style="width:100px;height:30px;">
</form>
</div> <!--Footer-->
</body>
</html>