{"id":9,"date":"2016-02-16T16:21:38","date_gmt":"2016-02-16T16:21:38","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=9"},"modified":"2016-02-16T16:21:38","modified_gmt":"2016-02-16T16:21:38","slug":"methodology","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=9","title":{"rendered":"Methodology"},"content":{"rendered":"
Last updated onTuesday, February 16, 2016<\/div>

Step 1: interrogating PB-PENTAdb database<\/h3>\n

The program will use a sliding window of 5 residues (pentapeptide) to parse every query protein sequences. For each pentapeptide, it will interrogate PB-PENTAdb<\/a> for its presence and get a list of all local structures (protein blocks) the pentapeptide is associated with. In absence of any hit, it will check in the database of the availability of the first 4 residues and will report any protein blocks they are associated with (see figure below).<\/p>\n

\"figure02b_kpred_database_query_and_hits\"<\/a><\/p>\n

Step 2: Methods for selecting among all possible PBs at each position<\/h3>\n

To select the best PB at each position, two methods were developed: (i) the majority rule method<\/strong> and (ii) the hybrid method<\/strong>. In the majority rule method<\/em>, it reports the most frequently occurring PB. In the hybrid method<\/em>, the most probable PB is reported by also taking into consideration the information of local structures of adjacent residues.<\/p>\n\n\n
\n

General scheme<\/h4>\n

\"figure02_scheme_for_kpred_predictions_using_pentadb\"<\/a>\n<\/td>\n

\n

Hybrid method<\/h4>\n

\"figure02c_kpred_hybrid_method\"<\/a>\n<\/td>\n<\/tr>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

Last updated onTuesday, February 16, 2016Step 1: interrogating PB-PENTAdb database The program will use a sliding window of 5 residues (pentapeptide) to parse every query protein sequences. For each pentapeptide, it will interrogate PB-PENTAdb for its presence and get a …<\/p>\n

Methodology<\/span> Read More »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"full-width-page.php","meta":{"footnotes":""},"class_list":["post-9","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7vx5Y-9","jetpack-related-posts":[{"id":26,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/","url_meta":{"origin":9,"position":0},"title":"PB-kpred","author":"adminufip","date":"April 1, 2016","format":false,"excerpt":"Knowledge-based prediction of local structures using protein blocks We have shown that protein 3D structure information can be abstracted advantageously into a simplified 1D representation in terms of a protein blocks sequence (PB-assignment). Indeed, it was shown previously by us (Tyagi et al, 2006, Tyagi et al, 2008) that the\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/kpred\/wp-content\/uploads\/2023\/04\/0C311915-43BC-4DB3-B376-03C3234889EB-300x225.jpeg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":7,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=7","url_meta":{"origin":9,"position":1},"title":"Help","author":"adminufip","date":"February 16, 2016","format":false,"excerpt":"Knowledge-based prediction of local structures using protein blocks PB-kPRED is a server for knowledge-based prediction of local backbone structures in terms of protein blocks (PBs). It is built upon the PB-PENTAdb database. Input Provide in the textbox one or more protein sequences in fasta format as shown below. Choice of\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"Screen Shot 2015-04-24 at 23.45.06","src":"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-24-at-23.45.06.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-24-at-23.45.06.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/Screen-Shot-2015-04-24-at-23.45.06.png?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":11,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=11","url_meta":{"origin":9,"position":2},"title":"Acknowledgements","author":"adminufip","date":"February 16, 2016","format":false,"excerpt":"Team PB-PENTAPEPT was developed and is maintained by an international team lead by Bernard Offmann (University of Nantes). Active members Nantes Universit\u00e9 (US2B, Nantes, France): Lionel Hoffmann, Yves-Henri Sanejouand, Bernard Offmann, Timoth\u00e9e Salzat-Hervouette INSERM and Universit\u00e9 Denis Diderot (DSIMB team, Paris, France): Alexandre G. de Brevern INSERM and Universit\u00e9 de\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/04\/LOGO-REGION-REUNION-150x150.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]}],"_links":{"self":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages\/9","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=9"}],"version-history":[{"count":1,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages\/9\/revisions"}],"predecessor-version":[{"id":10,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages\/9\/revisions\/10"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}