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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<link REL="SHORTCUT ICON" HREF="http://tanto.bioe.uic.edu/prelyscar/prelyscar.ico">
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />
<meta name="keywords" content="prelyscar, lysine carboxylation, prediction, predictor, tool, computational, Jimenez-Morales, David, Acta D, bioe, Liang lab, uic, chicago">
<meta name="description" content="Computational tool for the prediction of Lysine Carboxylation">
<meta name="author" content="David Jimenez-Morales">
<title>PreLysCar - Predictor of Lysine Carboxylation</title>
<style type="text/css">
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<style type="text/css">
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ga('create', 'UA-26635029-2', 'auto');
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<!-- STATS -->
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<script type="text/javascript">
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</head>
<body>
<table width="600" border="0" align="center" cellpadding="0" cellspacing="5">
<tr>
<td>
<table width="98%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td width="30%"><a href="http://www.uic.edu/uic/" target="_blank" class="style38 style41">University of Illinos at Chicago </a></td>
<td width="41%"><div align="center"><a href="http://gila.bioe.uic.edu/lab/" target="_blank" class="style37">Jie Liang Lab</a></div></td>
<td width="30%"><div align="right"><a href="http://www.bioe.uic.edu/BIOE/WebHome" target="_blank" class="style42">Department of Bioengineering</a></div></td>
</tr>
</table></td>
</tr>
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<td><table width="100%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<th width="42%" scope="row"><div align="center"><img src="images/urease200.jpg" width="200" height="200" /></div></th>
<td width="58%"><span class="style39">PreLysCar<br />
<span class="style40"><strong>Pre</strong>dictor of <strong>Lys</strong>ine <strong>Car</strong>boxylation</span></span></td>
</tr>
</table></td>
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<tr>
<td>
<div class="descriptor">Computational tool for the prediction of lysine carboxylation.</div>
</td>
</tr>
<tr>
<td><table width="62%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td scope="row">
<div align="left">
<p><strong>> Input:</strong> protein 3D coordinates in <span class="style51">PDB format</span>.<br />
<strong>> Output:</strong> lysine(s) residue(s) predicted as carboxylated.</p>
</div></td>
</tr>
</table></td>
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<tr>
<td><table width="75%" border="2" align="center" cellpadding="10" cellspacing="10" bordercolor="#006699" bgcolor="#CCCCFF">
<tr>
<td width="100%" class="submit">
<b>INPUT DATA</b> <br>
<form enctype="multipart/form-data" action="goprelyscar.php" method="post" onsubmit="return ray.ajax()">
<blockquote>
<p><i>Protein 3D coordinates (PDB format):</i><br>
<input type="file" name="uppdb">
</p>
<p> <i>Choose a probability:</i>
<SELECT name="prior">
<OPTION value="0.5">0.5</OPTION>
<OPTION value="0.05">0.05</OPTION>
<OPTION selected value="0.009">0.009</OPTION>
<OPTION value="0.0001">0.0001</OPTION>
</SELECT>
<span class="dropt"><em><b><u>Help</u></b></em>
<span style="width:300px;">
<b>How to choose the prior probability</b><br />
> A prior of <b>0.5</b> represents that the carboxylation of
lysine would have the same probability than a normal lysine,
which might result in more false positives (lysines incorrectly predicted as carboxylated).<br/>
>A prior of <b>0.0001</b> represents the opposite and less false positives should be expected<br/>
Our results with the training data set showed that <b>0.009</b> gave the best performance.
</span>
</span>
</p>
</blockquote>
<p align="center"><br>
<div id="load" style="display:none;">Uploading: Please wait</div>
<div align="center">
<input type=submit value=submit>
<br>
</p>
</div>
</form> </td>
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</table></td>
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<td> </td>
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<tr>
<td><table width="400" border="0" align="center">
<tr>
<td width="306" align="center"><strong>PreLysCar now <a href="http://www.ccp4.ac.uk/news/msg00205.html" target="_blank">available</a> at CCP4!</strong></td>
</tr>
<tr>
<td align="center"><img src="images/ccp4_logo.gif" width="203" height="80" alt=""/></td>
</tr>
<tr>
<td align="center"><span style="color: #2A5DC0"><strong><a href="http://www.ccp4.ac.uk/download/index.php" target="_blank">Download the last CCP4 version</a> to run PreLyscar locally</strong></span><strong>.</strong></td>
</tr>
</table></td>
</tr>
<tr>
<td><blockquote>
<div align="center"><span class="style46">PreLysCar, website, and interface developed by <a href="http://biodavidjm.github.io/" target="_blank">David Jimenez-Morales</a></span> <br />
<strong><a href="http://journals.iucr.org/d/issues/2014/01/00/lv5045/index.html" target="_blank" class="style42">Jimenez-Morales D, et.al. (2014). Acta Cryst. D 70, 48-57</a></strong><br />
<span class="style46"><a href='mailto:prelyscar@gmail.com?Subject=Comments about PreLysCar' target='_top'>Contact PreLysCar</a></span><br/>
</div>
</blockquote></td></tr>
</table>
</body>
</html>