{"id":7,"date":"2016-02-16T16:20:13","date_gmt":"2016-02-16T16:20:13","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=7"},"modified":"2023-04-03T12:54:42","modified_gmt":"2023-04-03T12:54:42","slug":"help","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=7","title":{"rendered":"Help"},"content":{"rendered":"
Last updated onMonday, April 3, 2023<\/div>

Knowledge-based prediction of local structures using protein blocks<\/h3>\n

<\/p>\n

PB-kPRED<\/a> is a server for knowledge-based prediction of local backbone structures in terms of protein blocks (PBs). It is built upon the PB-PENTAdb<\/a> database.<\/p>\n

Input<\/h3>\n

Provide in the textbox one or more protein sequences in fasta format as shown below.
\n\"Screen<\/a><\/p>\n

Choice of method<\/h3>\n

Choose one of the two methods available and click on submit button.
\nThe majority rule method is faster but is less precise. The hybrid method is more accurate but is slower. For details about these two methods, check here<\/a>.
\n\"Screen<\/a><\/p>\n

Waiting for results<\/h3>\n

If you chose the majority rule method, please wait for the results to display.
\nIf you chose the hybrid method, a new page opens and you have the option to provide an email address. This is highly recommended if you have more than 1 sequence or if your sequence is very long. An email will be sent with the job id and once the results are available, a new email will be sent with the link for the results. Click on “Launch kPRED hybrid” to launch the prediction.
\n\"Screen<\/a><\/p>\n

Results<\/h3>\n

On the result page, a table with sequence id, length of query protein, prediction score and estimated prediction accuracy are given (picture below).
\n\"kpred_results\"<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Last updated onMonday, April 3, 2023Knowledge-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 …<\/p>\n

Help<\/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-7","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7vx5Y-7","jetpack-related-posts":[{"id":26,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/","url_meta":{"origin":7,"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":9,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=9","url_meta":{"origin":7,"position":1},"title":"Methodology","author":"adminufip","date":"February 16, 2016","format":false,"excerpt":"Step 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 list of all local structures (protein blocks) the pentapeptide is associated with. In absence of\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"figure02b_kpred_database_query_and_hits","src":"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/figure02b_kpred_database_query_and_hits-1024x768.jpg?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\/figure02b_kpred_database_query_and_hits-1024x768.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/02\/figure02b_kpred_database_query_and_hits-1024x768.jpg?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":11,"url":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/?page_id=11","url_meta":{"origin":7,"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\/7","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=7"}],"version-history":[{"count":3,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages\/7\/revisions"}],"predecessor-version":[{"id":120,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=\/wp\/v2\/pages\/7\/revisions\/120"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/kpred\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}