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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> <html><head><title>CRNPRED: Prediction of One-dimensional Protein Structures (Secondary Structure, Contact Number, and Residue-wise Contact Order)</title ><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><link href="stylesheet/default.css" rel="stylesheet" type="text/css" /><link href="/favicon.ico" rel="icon" type="image/x-icon" /></head ><body><div class="title"><h1 class="title" title="CRNPRED top page"><a href="https://pdbj.org/"><img src="/cms-data/images/default.svg" alt="PDBj logo" width="100" /></a > CRNPRED </h1 ><h2 class="title">Prediction of One-dimensional Protein Structures: <br /><i>Secondary structures, contact numbers and residue-wise contact orders</i ><br /> [<a href="https://pdbj.org/help/crnpred" target="help">Help</a >]</h2 ></div ><div class="main">Given a query amino acid sequence, CRNPRED predicts one-dimensional structures including secondary structures, contact numbers and residue-wise contact orders, and returns the results via an email. For more information, please refer to the <a href="https://pdbj.org/help/crnpred" target="help">help</a > page.<h1>CRNPRED query submission</h1 ><form method="POST" enctype="multipart/form-data" action="/crnpred/"><input type="hidden" name="nonrest" value="yes" /><div id="query_frame"><div id="query_body"><div>Input amino acid sequence in the FASTA format: </div ><textarea name="fasta" cols="80" rows="10"></textarea ></div ><div id="query_example"><div>Query Example:</div ><pre>>test_sequence ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMP NMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLN KIFEKLGM</pre ></div ></div ><div class="clear"></div ><p id="predictor">Choose predictor: <select name="method"><option value="lin">Linear (fast, less accurate)</option ><option selected="selected" value="crnpred2k">CRN2000 (moderately fast and accurate)</option ><option value="crnpred5k">CRN5000 (slow, very accurate)</option ></select ></p ><p>Your email address: <input type="text" name="email" value="" size="35" /></p ><input type="submit" value="submit" /><input type="reset" value="reset" /></form ><hr size="3" /><h3>References</h3 ><ol><li><a href="https://doi.org/10.1186/1471-2105-7-401">CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.</a ><br />Kinjo, A. R.; Nishikawa, K. <em>BMC Bioinformatics </em ><strong>7</strong >:401 (2006) [Primary reference]</li ><li><a href="https://doi.org/10.2142/biophysics.1.67">Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks.</a ><br />Kinjo, A. R.; Nishikawa, K. <em>BIOPHYSICS </em ><strong>1</strong >:67-74 (2005) [Basic methodology]</li ><li><a href="https://doi.org/10.1093/bioinformatics/bti330">Recoverable one-dimensional encoding of three-dimensional protein structures.</a ><br />Kinjo, A. R.; Nishikawa, K. <em>Bioinformatics </em ><strong>21</strong >:2167-2170 (2005) [About one-dimensional structures]</li ></ol ><h3>Download software</h3 ><p>You can download the CRNPRED software from <a href="http://www.bioinformatics.org/crnpred/">http://www.bioinformatics.org/crnpred/</a ></p ><hr size="3" /><address align="right"><a href="https://pdbj.org/">Protein Data Bank Japan</a > 2009-06-10 (released) / 2009-10-14 (bug fix)</address ></div ></body ></html >