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1D protein structure prediction : Home Page
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} --></style> <link rel='stylesheet' href='https://www.bioinformatics.org/crnpred/wiki/pub/skins/bio/bio2.css' type='text/css' /><link rel='alternate' title='1D protein structure prediction RSS Feed' href='https://www.bioinformatics.org/crnpred/wiki/Main/AllRecentChanges?action=rss' type='application/rss+xml' /> <link rel='alternate' title='1D protein structure prediction Atom Feed' href='https://www.bioinformatics.org/crnpred/wiki/Main/AllRecentChanges?action=atom' type='application/atom+xml' /> <meta name='robots' content='index,follow' /> </head> <body> <!--PageHeaderFmt--> <table summary='Site Header' id='sitehead' cellpadding='0' cellspacing='0' border='0' align='center'> <tr> <td id='headleft' title='1D protein structure prediction Home'> <div id='headlogo'>1D protein structure prediction</div> </td> <td id='headright'> <div id='headcmdsupper'> <span class='headsearch'><a href='https://www.bioinformatics.org/crnpred/wiki/Site/Search' title='Search the site' rel='nofollow'>Search</a>: </span><form class='headsearch search' action='https://www.bioinformatics.org/crnpred/wiki'><input class='searchbox' type='text' name='q' value='' size='40' /><input class='searchbutton' type='submit' value='Go' /> <input type='hidden' name='n' value='Main.HomePage' /> <input type='hidden' name='action' value='search' /> </form></div> <div id='headcmdslower'> <span id='headbrowse'><a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage' title='Browse the page' rel='nofollow' accesskey='v'>View</a> | </span><span id='headedit'><a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=edit' title='Edit this page' rel='nofollow'>Edit</a> | </span><span id='headdiff'><a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=diff' title='History of this page' rel='nofollow'>History</a> | </span><span id='headabout'><a href='https://www.bioinformatics.org/crnpred/wiki/Main/AboutThisSite' title='About this site' rel='nofollow'>About 1D protein structure prediction</a></span></div> </td> </tr> </table> <!--/PageHeaderFmt--> <!--PageAdminTopFmt--><!--/PageAdminTopFmt--> <table summary='Site Main' id='sitemain' cellpadding='0' cellspacing='0' border='0' align='center'> <tr> <!--PageLeftFmt--> <td id='mainsidebar' > <table summary='SideBar' id='sidebar' width='100%' cellpadding='0' cellspacing='0' border='0'> <tr><td> <ul><li><a class='selflink' href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage'>HomePage</a> </li></ul><p class='vspace'></p><p class='sidehead' > CRNPRED </p><ul><li><a class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/Main/Download'>Download</a> </li><li><a class='urllink' href='http://crnpred.pdbj.org/' rel='nofollow'>Online prediction</a> </li><li><a class='urllink' href='http://bioinformatics.org/groups/?group_id=608' rel='nofollow'>BiO project page</a> </li></ul><p class='vspace'></p><p class='sidehead' > Project Wiki </p><ul><li><a class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/PmWiki/BasicEditing'>Basic Editing</a> </li><li><a class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/PmWiki/DocumentationIndex'>Documentation Index</a> </li><li><a class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/Main/WikiSandbox'>WikiSandbox</a> </li></ul><p class='vspace'></p><p style='text-align: right;' > <span style='font-size:83%'><a class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/Site/SideBar?action=edit'>edit SideBar</a></span> </p> <div id='sidebarbottom'><ul><li><span style='color: gray;' ><span style='font-size:83%'><a style='color: gray' class='wikilink' href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=login'>Login</a></span> </span> </li></ul> </div></td></tr> </table> </td> <!--/PageLeftFmt--> <td id='maincontent'> <table summary='Content' id='sitecontent' width='100%' cellpadding='0' cellspacing='0' border='0'> <tr><td> <!--PageTitleFmt--> <div id='location' title='Home Page was last modified on June 10, 2009, at 01:09 AM' ><span class='grouplink'>Main</span><span class='separator'>»</span><span class='titlelink'>Home Page</span></div> <div style='display:none;'><h1>Home Page</h1></div> <!--/PageTitleFmt--> <!--PageText--> <div id='wikitext'> <h2>CRNPRED: a software for accurate prediction of 1D protein structures.</h2> <p class='vspace'></p><p>CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence. </p> <p class='vspace'></p><p>The prediction scheme uses an output of PSI-BLAST (sequence profile), and is based on a novel machine learning technique called Critical Random Networks. </p> <p class='vspace'></p><p>For the methodology, refer to the following paper: </p><ul><li>A.R. Kinjo and K. Nishikawa, <strong>Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks</strong> <em>BIOPHYSICS</em>, <strong>1</strong>:67-74 (2005) <a class='urllink' href='http://dx.doi.org/10.2142/biophysics.1.67' rel='nofollow'>doi:10.2142/biophysics.1.67</a> </li></ul><p class='vspace'></p><p>The paper describing the software has been published as: </p><ul><li>A.R. Kinjo and K. Nishikawa, <strong>CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks</strong> <em>BMC Bioinformatics</em> <strong>7</strong>:401 (2006) <a class='urllink' href='http://dx.doi.org/10.1186/1471-2105-7-401' rel='nofollow'>doi:10.1186/1471-2105-7-401</a> </li></ul><p class='vspace'></p><p>CRNPRED predicts 3 types of 1D structures: SS, CN, and RWCO. To find out why these 3 types are of interest, refer to </p><ul><li>A.R. Kinjo and K. Nishikawa, <strong>Recoverable one-dimensional encoding of three-dimensional protein structures</strong> <em>Bioinformatics</em>, <strong>21</strong>:2167-2170 (2005) <a class='urllink' href='http://dx.doi.org/10.1093/bioinformatics/bti330' rel='nofollow'>doi:10.1093/bioinformatics/bti330</a> </li></ul><p class='vspace'></p><h2>Prediction Web Server</h2> <p class='vspace'></p><p>The web-based prediction service is available at </p><ul><li><span style='font-size:144%'> <a target='_blank' class='urllink' href='http://crnpred.pdbj.org/' rel='nofollow'>http://crnpred.pdbj.org/</a> </span> </li></ul> </div> </td></tr> </table> </td> <!--PageRightFmt--><!--/PageRightFmt--> </tr> </table> <!--PageAdminBtmFmt--><!--/PageAdminBtmFmt--> <table summary='Site Footer' id='sitefoot' cellpadding='0' cellspacing='0' border='0' align='center'> <!--PageFooterFmt--> <tr> <td id='footleft'> <span id='footeditsb'> <a href='https://www.bioinformatics.org/crnpred/wiki/Site/SideBar?action=edit' title='Edit the Side(B)ar' rel='nofollow' accesskey='b'>Edit SideBar</a> </span><span id='footedit'>| <a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=edit' title='(E)dit this page' rel='nofollow' accesskey='e'>Edit Page</a> </span><span id='foothist'>| <a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=diff' title='(H)istory of this page' rel='nofollow' accesskey='h'>Page History</a></span> </td> <td id='footmiddle'> <span id='footlastmod'>Page last modified on June 10, 2009, at 01:09 AM</span> </td> <td id='footright'> <span id='footchanges'><a href='https://www.bioinformatics.org/crnpred/wiki/Main/RecentChanges' title='Recent (C)hanges in this section' rel='nofollow' accesskey='c'>Recent Changes</a> <a href='https://www.bioinformatics.org/crnpred/wiki/Main/AllRecentChanges' title='(A)ll Recent changes for the entire site' rel='nofollow' accesskey='a'>(All)</a> </span><span id='footeditlogin'> | <a href='https://www.bioinformatics.org/crnpred/wiki/Main/HomePage?action=loginadmin' title='Admin Login' rel='nofollow'>Admin</a></span> </td> </tr> <!--/PageFooterFmt--> <tr> <td id='sitesole' colspan='3'> </td> </tr> </table> <!-- vim: expandtab sw=1 ts=1 sts=1 : --> </body> </html>