{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adfr\/?page_id=223"},"modified":"2019-10-09T17:43:27","modified_gmt":"2019-10-09T17:43:27","slug":"documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adfr\/documentation\/","title":{"rendered":"Documentation"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on October 9th, 2019 at 05:43 pm<\/p><p><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;--awb-margin-bottom:0px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h3><em>AutoDockFR<\/em> documentation<\/h3>\n<\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-bottom:20px;width:100%;\"><div class=\"fusion-separator-border sep-shadow\" style=\"--awb-height:20px;--awb-amount:20px;background:radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-webkit-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-moz-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-o-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2 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-1 fusion_builder_column_1_2 1_2 fusion-one-half fusion-column-first\" style=\"--awb-bg-size:cover;width:50%;width:calc(50% - ( ( 4% ) * 0.5 ) );margin-right: 4%;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-2\"><p><em>AutoDockFR<\/em> (or <em>ADFR<\/em> in short) is an open-source program for <a href=\"https:\/\/en.wikipedia.org\/wiki\/Docking_(molecular)\">docking<\/a> flexible ligands into receptors with selective flexibility. It is distribute as part of the <a href=\"https:\/\/ccsb.scripps.edu\/adfr\/downloads\/\"><em>ADFR<\/em> software suite<\/a> and implemented using a <a href=\"https:\/\/ccsb.scripps.edu\/adfr\/implementation\/\">re-usable software components<\/a> philosophy.<\/p>\n<\/div><div class=\"fusion-text fusion-text-3\"><h3>Step-by-step tutorials<\/h3>\n<\/div><div class=\"fusion-text fusion-text-4\"><p><strong>Prerequisites<\/strong>:<\/p>\n<ul>\n<li>You have\u00a0<a href=\"https:\/\/ccsb.scripps.edu\/adfr\/downloads\/\">downloaded and installed the ADFRsuite 1.0<\/a><\/li>\n<li>ADFRsuite-1.0\/bin in in your path\u00a0(if you use a command shell in Max OS, or Linux)<\/li>\n<li>you have downloaded and unzipped the\u00a0<a href=\"https:\/\/ccsb.scripps.edu\/agfr\/download\/551\/\">data file associated with this tutorial<\/a>.<\/li>\n<\/ul>\n<\/div><div class=\"fusion-content-boxes content-boxes columns row fusion-columns-1 fusion-columns-total-3 fusion-content-boxes-1 content-boxes-icon-on-side content-left\" style=\"--awb-body-color:#ffffff;--awb-title-color:#ffffff;--awb-hover-accent-color:#494e6b;--awb-circle-hover-accent-color:#494e6b;--awb-item-margin-bottom:40px;\" data-animationOffset=\"top-into-view\"><div style=\"--awb-backgroundcolor:#9acae0;--awb-content-padding-left:64px;\" class=\"fusion-column content-box-column content-box-column content-box-column-1 col-lg-12 col-md-12 col-sm-12 fusion-content-box-hover content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-redocking\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-redocking\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;padding-left:64px;\">Hello docking ! a first example fo re-docking a ligand with ADFR<\/h3><\/a><\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;--awb-content-padding-left:64px;\" class=\"fusion-column content-box-column content-box-column content-box-column-2 col-lg-12 col-md-12 col-sm-12 fusion-content-box-hover content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/adfr\/flexible-receptor\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/adfr\/flexible-receptor\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;padding-left:64px;\">Docking with flexible receptor side chains<\/h3><\/a><\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;--awb-content-padding-left:64px;\" class=\"fusion-column content-box-column content-box-column content-box-column-3 col-lg-12 col-md-12 col-sm-12 fusion-content-box-hover content-box-column-last content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-covalent\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-covalent\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;padding-left:64px;\">Docking a covalently bound ligand<\/h3><\/a><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_2 1_2 fusion-one-half fusion-column-last\" style=\"--awb-bg-size:cover;width:50%;width:calc(50% - ( ( 4% ) * 0.5 ) );\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-title title fusion-title-1 fusion-sep-none fusion-title-text fusion-title-size-one\" style=\"--awb-margin-top-small:10px;--awb-margin-right-small:0px;--awb-margin-bottom-small:10px;--awb-margin-left-small:0px;\"><h1 class=\"fusion-title-heading title-heading-left\" style=\"margin:0;\"><h3 style=\"text-align: center;\">FAQ<\/h3><\/h1><\/div><div class=\"fusion-text fusion-text-5\"><ol>\n<li><a href=\"https:\/\/ccsb.scripps.edu\/adfr\/how-to-create-a-pdbqt-for-my-receptor\/\" target=\"_blank\" rel=\"noopener\">How to create a PDBQT for a rigid receptor<\/a><\/li>\n<\/ol>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This page was last updated on October 9th, 2019 at  [&#8230;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-223","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/223","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/comments?post=223"}],"version-history":[{"count":34,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/223\/revisions"}],"predecessor-version":[{"id":1117,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/223\/revisions\/1117"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/media?parent=223"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}