{"id":52,"date":"2012-04-17T17:17:39","date_gmt":"2012-04-17T17:17:39","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=52"},"modified":"2023-05-03T09:12:43","modified_gmt":"2023-05-03T09:12:43","slug":"pb-svindex-home","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=52","title":{"rendered":"PB-SVindex home"},"content":{"rendered":"<p><strong><em>PB-SVindex : knowledge-based calculation of Structural Variability Indices of pentapeptide sequences<\/em><\/strong><\/p>\n<p>This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from <a href=\".\/?page_id=25\">PB-PENTAdb<\/a> database to calculate a structural variability index (SVI) for each of them. It shows if a pentapeptide is observed to have multiple local conformations in terms of PBs or not.<\/p>\n<p>This proposed index is similar to the <strong>Simpson&#8217;s diversity index<\/strong> used in population genetics :<\/p>\n<p><a href=\"..\/pentapept\/wp-content\/uploads\/2010\/08\/simpson-index.png\"><img decoding=\"async\" class=\"alignnone size-full wp-image-981\" title=\"simpson index\" src=\"..\/pentapept\/wp-content\/uploads\/2010\/08\/simpson-index.png\" alt=\"\"><\/a><\/p>\n<p><em>pi<\/em> is the fraction of all organisms which belong to the <em>i<\/em>-th species<\/p>\n<p>Here we calculate SVI using an approximation of Simpson&#8217;s index :<\/p>\n<p><a href=\"..\/pentapept\/wp-content\/uploads\/2010\/08\/simpson-3.png\"><img loading=\"lazy\" decoding=\"async\" src=\"..\/pentapept\/wp-content\/uploads\/2010\/08\/simpson-3.png\" alt=\"\" title=\"simpson 3\" class=\"alignnone size-full wp-image-1009\" width=\"150\" height=\"60\"><\/a><\/p>\n<p>where, for a given amino acid motif, <em>ni<\/em> is its occurence in PB class <em>i<\/em>, and <em>n<\/em> is the total number of times this motif is found in the database.<br \/>\nThis is an estimator for Simpson&#8217;s index for sampling without replacement.<\/p>\n<p>Assigned variability index values vary between 0 and 1. Lower values indicate sequences with low structural variability, higher values indicate higher structural variability.<\/p>\n<hr>\n<p><strong>Search by SCOP domain ID: <\/strong><\/p>\n<form action=\"\/cgi-bin\/penta175\/pb_pred2\/pbflexPRED.cgi\" method=\"post\">\n<textarea name=\"domain\" maxlength=\"7\">d1dlwa_<\/textarea><br \/>\n<input type=\"submit\" value=\"Submit\"><br \/>\n<\/form>\n<p>As output, a table is provided with<\/p>\n<ul>\n<li>Sequence<\/li>\n<li>SV index<\/li>\n<li>Backbone B-factor<\/li>\n<li>Relative Surface Accessibility (RSA)<\/li>\n<\/ul>\n<hr>\n<p><strong>Search by entering your amino acid sequences in fasta format (max 1000 sequences) :<\/strong><\/p>\n<form action=\"\/cgi-bin\/penta175\/pb_pred2\/pbflexPRED.cgi\" method=\"post\">\n<textarea cols=\"120\" rows=\"8\" name=\"pentapeptide\" style=\"font-family:courier\"><\/textarea><br \/>\n<input type=\"submit\" value=\"Submit\"><br \/>\n<\/form>\n<p>As output, a table is provided with<\/p>\n<ul>\n<li>first 8 characters of ID of sequence (it removes the &#8220;&gt;&#8221; from first line),<\/li>\n<li>SV index<\/li>\n<\/ul>\n<p>with SVI values separated by comas.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>PB-SVindex : knowledge-based calculation of Structural Variability Indices of pentapeptide sequences This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from PB-PENTAdb database to calculate a structural variability index (SVI) for each of them. It shows if a pentapeptide is observed to have multiple local conformations in terms of PBs [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":48,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"page-without-sidebar.php","meta":{"footnotes":""},"class_list":["post-52","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/52","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=52"}],"version-history":[{"count":8,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/52\/revisions"}],"predecessor-version":[{"id":272,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/52\/revisions\/272"}],"up":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/48"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=52"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}