{"id":105,"date":"2012-02-16T13:14:34","date_gmt":"2012-02-16T13:14:34","guid":{"rendered":"http:\/\/.\/?page_id=105"},"modified":"2023-04-13T09:29:11","modified_gmt":"2023-04-13T09:29:11","slug":"pb-pentapept-help","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/?page_id=105","title":{"rendered":"PB-PENTAdb Help"},"content":{"rendered":"<div class=\"post-meta\">Last update on Thursday, April 13, 2023<\/div><p>The general scheme used to build <a href=\".\/?page_id=4\">PB-PENTAdb<\/a> is summarized in the diagram below :<\/p>\n<p><a href=\".\/wp-content\/uploads\/2010\/08\/pentapeptide_database_construction_process_Aug2011.png\"><img loading=\"lazy\" decoding=\"async\" src=\".\/wp-content\/uploads\/2010\/08\/pentapeptide_database_construction_process_Aug2011.png\" alt=\"pentapeptide database construction process\" title=\"pentapeptide database construction process\" class=\"aligncenter size-full wp-image-1835\" width=\"640\" height=\"450\"><\/a><\/p>\n<p>The database hence contains the following features for each pentapeptide :<\/p>\n<ul>\n<li>protein id<\/li>\n<li>the PB class<\/li>\n<li>the position of the first residue of the pentapeptide in the pdb-style SCOP file<\/li>\n<li>the dihedral angles (phi and psi values)<\/li>\n<li>the lowest angular rmsd (rmsda) between pentapeptide&#8217;s dihedral angles and standard dihedral angles of PBs<\/li>\n<li>the secondary structure assignments (from <a href=\"http:\/\/swift.cmbi.ru.nl\/gv\/dssp\/\" title=\"DSSP website\" target=\"_blank\" rel=\"noopener\">DSSP<\/a>)<\/li>\n<li>a series of 5 values corresponding to the &#8220;all atoms&#8221; relative solvent accessibility for all 5 residues<\/li>\n<li>a series of 5 values corresponding to backbone B factors of 5 residues<\/li>\n<\/ul>\n<h2>Simplified query tool<\/h2>\n<p><strong>Input:<\/strong> Enter a valid pentapeptide sequence (5 residues long) in the text area with no space between the residues. You can use the underscore &#8220;_&#8221; sign to specify &#8220;any&#8221; residue. You can choose to search in datasets filtered at different sequence similarity cutoffs.<\/p>\n<p><a href=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-22-at-23.38.14.png?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-22-at-23.38.14.png?resize=480%2C420&#038;ssl=1\" alt=\"Screen Shot 2015-04-22 at 23.38.14\" class=\"aligncenter size-full wp-image-603\" width=\"480\" height=\"420\" srcset=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-22-at-23.38.14.png?resize=100%2C87&amp;ssl=1 100w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-22-at-23.38.14.png?resize=150%2C130&amp;ssl=1 150w\" sizes=\"auto, (max-width: 480px) 100vw, 480px\" \/><\/a><\/p>\n<p>The results are delivered as followed :<\/p>\n<p><a href=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=605%2C662&#038;ssl=1\" alt=\"PB-PENTAPEPT\" class=\"aligncenter size-large wp-image-605\" width=\"605\" height=\"662\" srcset=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=936%2C1024&amp;ssl=1 936w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=274%2C300&amp;ssl=1 274w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=100%2C109&amp;ssl=1 100w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=150%2C164&amp;ssl=1 150w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=200%2C219&amp;ssl=1 200w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=300%2C328&amp;ssl=1 300w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=450%2C492&amp;ssl=1 450w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=600%2C656&amp;ssl=1 600w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?resize=900%2C984&amp;ssl=1 900w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?w=1210&amp;ssl=1 1210w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/PB-PENTAPEPT.jpg?w=1815&amp;ssl=1 1815w\" sizes=\"auto, (max-width: 605px) 100vw, 605px\" \/><\/a><\/p>\n<p>Different links provided on the result page are described in the following figure<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/link.png\" target=\"_blank\" rel=\"noopener\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/link.png\" alt=\"Links\"><\/a><\/p>\n<h2> SQL Advanced Query<\/h2>\n<p>The user can also provide <strong>more elaborated queries<\/strong> to the database in the second section of the tool :<\/p>\n<p><a href=\".\/wp-content\/uploads\/2012\/02\/sql_query.png\" target=\"_blank\" rel=\"noopener\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/sql_query.png\" alt=\"SQL Query\"><\/a><\/p>\n<p><strong>Input: <\/strong>Enter a mysql command. DO NOT put a semi colon (;) at the end of your command line.<br \/>\n<em>example :<\/em> SELECT pb, COUNT(*) AS number FROM mapping100 GROUP BY pb<br \/>\nThe table containing the data is called <em>mapping100<\/em>.<br \/>\nThe structure of the table is as follows :<\/p>\n<table>\n<tbody>\n<tr>\n<td><strong>Field<\/strong><\/td>\n<td>id_protein<\/td>\n<td>pb<\/td>\n<td>aaseq<\/td>\n<td>pos<\/td>\n<td>psi1<\/td>\n<td>phi2<\/td>\n<td>psi2<\/td>\n<td>phi3<\/td>\n<td>psi3<\/td>\n<td>phi4<\/td>\n<td>psi4<\/td>\n<td>phi5<\/td>\n<\/tr>\n<tr>\n<td><strong>Type<\/strong><\/td>\n<td>varchar(20)<\/td>\n<td>varchar(4)<\/td>\n<td>varchar(9)<\/td>\n<td>int(11)<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>int(11)<\/td>\n<\/tr>\n<tr>\n<td><strong>Field<\/strong><\/td>\n<td>rmsda<\/td>\n<td>sec_str<\/td>\n<td>rsa1<\/td>\n<td>rsa3<\/td>\n<td>rsa3<\/td>\n<td>rsa4<\/td>\n<td>rsa5<\/td>\n<\/tr>\n<tr>\n<td><strong>Type<\/strong><\/td>\n<td>float<\/td>\n<td>varchar(5)<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>Description of the <em>rmsda100<\/em> table in our database :<\/p>\n<table>\n<tbody>\n<tr>\n<td><strong>Field<\/strong><\/td>\n<td>id_protein<\/td>\n<td>pb<\/td>\n<td>aaseq<\/td>\n<td>pos<\/td>\n<td>CA_Bfac1<\/td>\n<td>CA_Bfac2<\/td>\n<td>CA_Bfac3<\/td>\n<td>CA_Bfac4<\/td>\n<\/tr>\n<tr>\n<td><strong>Type<\/strong><\/td>\n<td>varchar(20)<\/td>\n<td>varchar(4)<\/td>\n<td>varchar(9)<\/td>\n<td>int(11)<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<\/tr>\n<tr>\n<td><strong>Field<\/strong><\/td>\n<td>CA_Bfac5<\/td>\n<td>Bkbone_Bfac1<\/td>\n<td>Bkbone_Bfac2<\/td>\n<td>Bkbone_Bfac3<\/td>\n<td>Bkbone_Bfac4<\/td>\n<td>Bkbone_Bfac5<\/td>\n<td>pb1<\/td>\n<td>rmsda1<\/td>\n<\/tr>\n<tr>\n<td><strong>Type<\/strong><\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>float<\/td>\n<td>varchar(4)<\/td>\n<td>float<\/td>\n<\/tr>\n<tr>\n<td><strong>Field<\/strong><\/td>\n<td>pb2<\/td>\n<td>rmsda2<\/td>\n<\/tr>\n<tr>\n<td><strong>Type<\/strong><\/td>\n<td>varchar(4)<\/td>\n<td>float<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>Results:<\/strong> output is according to user&#8217;s query and is downloadable.<\/p>\n<h2> Advanced Query<\/h2>\n<p>User can choose to fill required fields and leave the other fields which are not required as they are. User can get help about a particular field if he gets the mouse pointer over that field&#8217;s text box. e.g. Help about sequence field is shown in the image below.<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/adv_search.png\" target=\"_blank\" rel=\"noopener\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/adv_search.png\" alt=\"Advanced Search\"><\/a><\/p>\n<p>User can also choose the fields to be displayed in the result.<br \/>\n<a href=\".\/wp-content\/uploads\/2012\/02\/adv_display.png\" target=\"_blank\" rel=\"noopener\"><img decoding=\"async\" src=\".\/wp-content\/uploads\/2012\/02\/adv_display.png\" alt=\"Output Fields\"><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Last update on Thursday, April 13, 2023The general scheme used to build PB-PENTAdb is summarized in the diagram below : The database hence contains the following features for each pentapeptide : protein id the PB class the position of the &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"more-link\" href=\"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/?page_id=105\"> <span class=\"screen-reader-text\">PB-PENTAdb Help<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":49,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"full-width-page.php","meta":{"footnotes":""},"class_list":["post-105","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/105","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=105"}],"version-history":[{"count":40,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/105\/revisions"}],"predecessor-version":[{"id":801,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/105\/revisions\/801"}],"up":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=\/wp\/v2\/pages\/49"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=105"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}