{"id":3276,"date":"2024-02-13T07:12:10","date_gmt":"2024-02-13T07:12:10","guid":{"rendered":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/?p=3276"},"modified":"2024-02-13T10:08:27","modified_gmt":"2024-02-13T10:08:27","slug":"rippmine-nii","status":"publish","type":"post","link":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/rippmine-nii\/","title":{"rendered":"RiPPMine, NII"},"content":{"rendered":"\n

RiPPMiner<\/strong>\u00a0is a machine learning based webserver for deciphering chemical structures of Ribosomally synthesized Post translationally modified Peptides (RiPPs) which constitute one of the major class of pharmaceutically important antimicrobial compounds (e.g. NisinA). It uses amino acid sequence of the precursor polypeptide of RiPPs as input.
Tools:<\/strong>\u00a0RIPPMiner uses SVM to classify the precursor into nine sub-classes of RiPPs. For classes like\u00a0Lanthipeptide<\/strong>,\u00a0Cyanobactin<\/strong>\u00a0and\u00a0Lassopeptide<\/strong>, RiPPMiner predicts the leader cleavage site and finally complex crosslinking and post-translationally modified residues are predicted in the core peptide. For\u00a0Thiopeptide<\/strong>\u00a0it predicts crosslinking and modified residues. RiPPMiner can identify correct PTM and crosslink pattern in a query RiPP core peptide from among a very large number of combinatorial possibilities using machine learning. RiPPMiner also provides GUI for visualization of the predicted chemical structure and also search for characterized RiPPs similar to a given peptide sequence or a given chemical structure.
Database:<\/strong>\u00a0RiPPMiner derives its predictive power from training using a manually curated database of more than\u00a0500+<\/strong>\u00a0experimentally characterized RiPPs belonging to\u00a013 Subclasses<\/strong>. These Classes include\u00a0Lanthipeptide<\/a>,\u00a0Bottromycin<\/a>,\u00a0Cyanobactin<\/a>,\u00a0Glycocin<\/a>,\u00a0Lassopeptide<\/a>,\u00a0Linaridin<\/a>,\u00a0Linearazol<\/a>,\u00a0Microcin<\/a>,\u00a0Sactipeptide<\/a>,\u00a0Thiopeptide<\/a>,\u00a0Auto Inducing Peptide<\/a>,\u00a0ComX<\/a>,\u00a0Bacterial Head to Tail Cyclized<\/a>. Each RiPP has information like\u00a0Modification System,\u00a0Complete Sequence,\u00a0Leader\u00a0and\u00a0Core Sequence,\u00a0modified residues,\u00a0Cross-links,\u00a0Pubmed,\u00a0PDB ID,\u00a0Gene Cluster\u00a0among others.<\/p>\n\n\n\n

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RiPPMiner\u00a0is a machine learning based webserver for deciphering chemical structures of Ribosomally synthesized Post translationally modified Peptides (RiPPs) which constitute […]<\/p>\n","protected":false},"author":1,"featured_media":3281,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}}},"categories":[54],"tags":[],"_links":{"self":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/posts\/3276"}],"collection":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/comments?post=3276"}],"version-history":[{"count":1,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/posts\/3276\/revisions"}],"predecessor-version":[{"id":3289,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/posts\/3276\/revisions\/3289"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/media\/3281"}],"wp:attachment":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/media?parent=3276"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/categories?post=3276"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/tags?post=3276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}