{"id":385,"date":"2019-08-01T14:30:46","date_gmt":"2019-08-01T14:30:46","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/autodock\/?page_id=385"},"modified":"2024-11-14T23:42:08","modified_gmt":"2024-11-14T23:42:08","slug":"tools-methods","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/autodocksuite\/tools-methods\/","title":{"rendered":"Tools &#038; Methods"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><p>There have been various tools and methods developed to assist with setup, docking and analysis with AutoDock and Vina. A collection of such resources for legacy AutoDock4.2.6 and Vina v1.1.2 can be found at:<\/p>\n<p><a href=\"https:\/\/autodock.scripps.edu\/resources\/\">https:\/\/autodock.scripps.edu\/resources\/<\/a><\/p>\n<p>More recently, the Forli lab have been developing <strong>command-line tools and Python bindings<\/strong> for interoperability with RDKit, SQLite and other modern cheminformatics utility tools:<\/p>\n<p><strong>Meeko: <a href=\"https:\/\/github.com\/forlilab\/Meeko\">https:\/\/github.com\/forlilab\/Meeko<\/a><\/strong><\/p>\n<p>Meeko streamlines the processing of ligand coordinate files for use in docking. It reads an RDKit molecule object and writes a PDBQT string (or file) for <a href=\"https:\/\/github.com\/ccsb-scripps\/AutoDock-Vina\">AutoDock-Vina<\/a>\u00a0and\u00a0<a href=\"https:\/\/github.com\/ccsb-scripps\/AutoDock-GPU\">AutoDock-GPU<\/a>. It converts the docking output to RDKit molecules and SD files, without loss of bond orders.<\/p>\n<p><strong>Ringtail: <a href=\"https:\/\/github.com\/forlilab\/Ringtail\">https:\/\/github.com\/forlilab\/Ringtail<\/a><\/strong><\/p>\n<p>Ringtail reads collections of Docking Log Files (DLG) or PDBQT results from virtual screenings performed with <a href=\"https:\/\/github.com\/ccsb-scripps\/AutoDock-GPU\">AutoDock-GPU<\/a>\u00a0and\u00a0<a href=\"https:\/\/github.com\/ccsb-scripps\/AutoDock-Vina\">AutoDock-Vina<\/a>, respectively, and deposits them into a SQLite database. It then allows for the filtering of results with numerous pre-defined filtering options, generation of a simple result scatterplot, export of molecule SDFs, and export of CSVs of result data. Result file parsing is parallelized across the user\u2019s CPU.<\/p>\n<p>For the latest developments and information, please visit the linked project Github pages or our new navigation &amp; resource site at <a href=\"https:\/\/rsd3.scripps.edu\/\">https:\/\/rsd3.scripps.edu\/<\/a>.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-385","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/385","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/comments?post=385"}],"version-history":[{"count":6,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/385\/revisions"}],"predecessor-version":[{"id":515,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/385\/revisions\/515"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/media?parent=385"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}