{"id":2,"date":"2012-04-17T13:59:39","date_gmt":"2012-04-17T13:59:39","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=2"},"modified":"2023-05-05T14:58:35","modified_gmt":"2023-05-05T14:58:35","slug":"sample-page","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/","title":{"rendered":"PBE home"},"content":{"rendered":"<p><a href=\"https:\/\/www.univ-reunion.fr\/\" target=\"_blank\" rel=\"noopener\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"alignright\" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/04\/logo_univ_reunion.jpg?resize=45%2C40&#038;ssl=1\" alt=\"\" width=\"45\" height=\"40\" \/><\/a><a href=\"https:\/\/www.cnrs.fr\/fr\" target=\"_blank\" rel=\"noopener\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"alignright\" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pentapept\/wp-content\/uploads\/2012\/04\/logo-cnrs.jpg?resize=40%2C40&#038;ssl=1\" alt=\"\" width=\"40\" height=\"40\" \/><\/a><a href=\"https:\/\/us2b.univ-nantes.fr\/\" target=\"_blank\" rel=\"noopener\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-262 \" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2023\/05\/logo_us2b-e1683038698993.webp?resize=84%2C46&#038;ssl=1\" alt=\"\" width=\"84\" height=\"46\" \/><\/a><a href=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-101\" src=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?resize=600%2C342&#038;ssl=1\" alt=\"PBE2.0 figure\" width=\"600\" height=\"342\" srcset=\"https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?resize=1024%2C585&amp;ssl=1 1024w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?resize=300%2C171&amp;ssl=1 300w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?w=2000&amp;ssl=1 2000w, https:\/\/i0.wp.com\/pbpred-us2b.univ-nantes.fr\/pbe\/wp-content\/uploads\/2012\/04\/PBE2.0.jpg?w=3000&amp;ssl=1 3000w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/a><br \/>\nPBE server 2.0 aims to provide a platform for <strong>protein structure\u00a0analysis and comparison<\/strong> using well defined library of short structural motifs (SSMs)\u00a0known as\u00a0structural alphabets\u00a0(SA). It uses a set of 16 SSMs called\u00a0<strong>Protein Blocks<\/strong> (PBs) and a\u00a0PB substitution matrix\u00a0derived\u00a0from large set of structurally aligned homologous proteins present in <a href=\"http:\/\/pauling.mbu.iisc.ernet.in\/%7Epali\/pmain.html\" target=\"_blank\" rel=\"noopener\">PALI<\/a> database.<\/p>\n<p>PBE international development team is composed of : <em>Swapnil Mahajan, Manoj Tyagi, Priyanka Sharma, Murielle Grondin, Matthieu Drula, Aurore Va\u00eftinadapoull\u00e9, Etienne Frumence, Fr\u00e9d\u00e9ric Cadet, N. Srinivasan, Alexandre G. de Brevern and Bernard Offmann<\/em> and is developed jointly with <a href=\"http:\/\/www.peaccel.com\/\">PEACCEL Inc.<\/a><\/p>\n<h3>Features<\/h3>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li><a href=\".\/?page_id=10\" target=\"_blank\" rel=\"noopener\"><strong>PBE-T<\/strong> &#8211; Transformation of protein structure 3D information into 1D sequence of PBs<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<blockquote><p><strong>Protein structure comparison<\/strong><\/p>\n<ul>\n<li><a href=\".\/?page_id=12\"><strong>PB-ALIGNc<\/strong> \u2013 Structure comparison tool to identify local or global structural similarities between two protein structures<\/a><\/li>\n<li><a href=\".\/?page_id=12\"><strong>PB-ALIGNm<\/strong> \u2013 Structure mining tool to identify proteins with similar fold from structural database given a query structure<\/a><\/li>\n<li><a href=\"http:\/\/www.dsimb.inserm.fr\/dsimb_tools\/ipba\/\"><strong>iPBA<\/strong> &#8211; also kindly consider to use iPBA server which has strong improvements with respects to PB-ALIGN. The algorithm search of anchors regions.<\/a><\/li>\n<li><a title=\"Multiple alignment using protein blocks\" href=\"http:\/\/www.dsimb.inserm.fr\/dsimb_tools\/mulpba\/\" target=\"_blank\" rel=\"noopener\"><strong>mulPBA<\/strong> &#8211; Multiple alignment using protein blocks. It extends the method behind iPBA to multiple structural alignments.<\/a><\/li>\n<\/ul>\n<\/blockquote>\n<ul>\n<li><a href=\".\/?page_id=25\" target=\"_blank\" rel=\"noopener\"><strong>PBE-PENTAdb<\/strong> &#8211; A database for analysis of structural diversity of pentpeptides in terms of PBs<\/a><\/li>\n<li><a href=\".\/?page_id=37\" target=\"_blank\" rel=\"noopener\"><strong>PBE-kPRED<\/strong> &#8211; Knowledge-based tool for predicting local structure in terms of PBs<\/a><\/li>\n<li><a href=\".\/?page_id=52\" target=\"_blank\" rel=\"noopener\"><strong>PBE-PB-<em>SVindex<\/em><\/strong> &#8211; structural diversity of pentapeptides in protein structures.<\/a><\/li>\n<li><strong>DoSA<\/strong> &#8211; Database of structural alignments of structurally variable regions (currently unavailable)<\/li>\n<li><a title=\"Fold Recognition using a Structural Alphabet\" href=\"https:\/\/protsci-us2b.univ-nantes.fr\/forsa\/\" target=\"_blank\" rel=\"noopener\"><strong>FoRSA<\/strong> &#8211; Protein fold recognition using protein blocks<\/a><\/li>\n<\/ul>\n<h3>References<\/h3>\n<ol>\n<li><a href=\"http:\/\/www.bernardoffmann.fr\/?p=459\">Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern and Narayanaswamy Srinivasan. DoSA: Database of Structural Alignments. <em>Database<\/em> (2013).<\/a><\/li>\n<li><a title=\"Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure\" href=\".\/?p=337\">Swapnil Mahajan, Alexandre G. de Brevern, Bernard Offmann and Narayanaswamy Srinivasan. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. <i>Journal of Biomolecular Structure &amp; Dynamics<\/i> (2013), in press.<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21586582\">Gelly JC, Joseph AP, Srinivasan N, de Brevern AG. iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res. 2011, 39(Web Server issue):W18-23.<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21731588\">Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Fr\u00e9d\u00e9ric Cadet, Aur\u00e9lie Bornot, Manoj Tyagi and H\u00e9l\u00e8ne Valadi\u00e9, et al. A short survey on protein blocks. Biophysical Reviews (2010) <strong>2<\/strong>(3):137-145<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19625218\">Protein short loop prediction in terms of a structural alphabet. Tyagi M, Bornot A, Offmann B, de Brevern AG.\u00a0Comput Biol Chem. (2009) 33(4):329-33.<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18004784?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&amp;ordinalpos=7\" target=\"_blank\" rel=\"noopener\">Tyagi M., de Brevern A.G., Srinivasan N.,\u00a0Offmann B.\u00a0Protein structure mining using a structural alphabet. <em>Proteins <\/em>71:920\u2013937, (2008).<\/a><\/li>\n<li>Offmann B., Tyagi M., de Brevern A.G.\u00a0Local Protein Structures.\u00a0<em>Current Bioinformatics, <\/em>2, 165-202, 2007.<\/li>\n<li><a href=\"http:\/\/eutils.ncbi.nlm.nih.gov\/entrez\/eutils\/elink.fcgi?dbfrom=pubmed&amp;id=16894618&amp;retmode=ref&amp;cmd=prlinks\">Tyagi M,\u00a0Gowri V.S., Srinivasan N, \u00a0de Brevern A.G, &amp;\u00a0Offmann B. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. <em>Proteins<\/em> 65(1) :32-39, (2006).<\/a><\/li>\n<li><a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/content\/full\/34\/suppl_2\/W119\">Tyagi M,\u00a0Sharma P, Swamy C.S, Cadet F, Srinivasan N, de Brevern A.G. and Offmann B. Protein Block Expert (PBE).\u00a0A web-based protein structure analysis server using a structural alphabet. <em>Nucleic Acids Res.<\/em>, 34:W119-W123, (2006).<\/a><\/li>\n<li>de Brevern A.G. New assessment of a structural alphabet.\u00a0<em>In Silico Biology<\/em>, 5, 26, (2005).<\/li>\n<li>de Brevern A.G, Etchebest C. and Hazout S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. <em>Proteins<\/em> 41:271-287, (2000).<\/li>\n<\/ol>\n<address>Site maintained by : <a title=\"email to Bernard Offmann\" href=\"mailto:bernard.offmann@univ-nantes.fr\">B. Offmann<\/a><\/address>\n<p>&#8211;&gt;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>PBE server 2.0 aims to provide a platform for protein structure\u00a0analysis and comparison using well defined library of short structural motifs (SSMs)\u00a0known as\u00a0structural alphabets\u00a0(SA). It uses a set of 16 SSMs called\u00a0Protein Blocks (PBs) and a\u00a0PB substitution matrix\u00a0derived\u00a0from large set of structurally aligned homologous proteins present in PALI database. PBE international development team is composed [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"page-without-sidebar.php","meta":{"footnotes":""},"class_list":["post-2","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\/2","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=2"}],"version-history":[{"count":61,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/2\/revisions"}],"predecessor-version":[{"id":273,"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=\/wp\/v2\/pages\/2\/revisions\/273"}],"wp:attachment":[{"href":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}