{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/crankpep\/?page_id=223"},"modified":"2019-06-04T00:28:58","modified_gmt":"2019-06-04T00:28:58","slug":"documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adcp\/documentation\/","title":{"rendered":"Documentation"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on June 4th, 2019 at 12:28 am<\/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>AutoDock CrankPep<\/em>\u00a0documentation<\/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>AutoDock CrankPep<\/em>\u00a0(or <em>ADCP<\/em>\u00a0in short) is an open-source program for <a href=\"https:\/\/en.wikipedia.org\/wiki\/Docking_(molecular)\">docking<\/a> flexible peptides into receptors. The latest source code is updated on <a href=\"https:\/\/github.com\/ccsb-scripps\/ADCP\">GitHub<\/a>.<\/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\/adcp\/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\/adcp\/download\/1063\/\">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-1 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 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\/adcp\/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\/adcp\/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;\">A redocking experiment of a 7-mer peptide<\/h3><\/a><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><div class=\"fusion-content-boxes content-boxes columns row fusion-columns-1 fusion-columns-total-1 fusion-content-boxes-2 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 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\/adcp\/tutorial-cyclic\/\" 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\/adcp\/tutorial-cyclic\/\" 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;\">A redocking experiment of a cyclic peptide<\/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><style type=\"text\/css\">#accordian-1 .fusion-panel:hover,#accordian-1 .fusion-panel.hover{ background-color: #f9f9f9 } #accordian-1 .fusion-panel { border-color:#494e6b; border-width:1px; background-color:#494e6b; }.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box:before{ font-size: 13px;width: 13px;}.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box{ color: #000000;}.fusion-accordian  #accordian-1 .panel-title a{font-family:\"Montserrat\";font-style:normal;font-weight:400;}.fusion-accordian  #accordian-1 .panel-title a:not(:hover){}.fusion-accordian  #accordian-1 .toggle-content{font-family:\"Hind\";font-style:normal;font-weight:400;}.fusion-accordian #accordian-1 .fa-fusion-box { background-color: #e91e63 !important;border-color: #e91e63 !important;}.fusion-accordian #accordian-1 .panel-title a:hover,.fusion-accordian #accordian-1 .panel-title a.hover { color: #337d93;}.fusion-faq-shortcode .fusion-accordian #accordian-1 .fusion-toggle-boxed-mode:hover .panel-title a { color: #337d93;}.fusion-accordian #accordian-1 .panel-title .active .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a:hover .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a.hover .fa-fusion-box { background-color: #337d93!important;border-color: #337d93!important;}<\/style><div class=\"fusion-faq-shortcode\" style=\"\"><div class=\"fusion-faqs-wrapper\"><div class=\"accordian fusion-accordian\"><div class=\"panel-group \" id=\"accordian-1\"><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-1167 \"><span class=\"entry-title rich-snippet-hidden\">FAQ for ADCP<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/adcp\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-07-22T19:02:09+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-1167\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-1167\" href=\"#collapse-1-1167\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">FAQ for ADCP<\/div><\/a><\/h4><\/div><div id=\"collapse-1-1167\" aria-labelledby=\"faq_1-1167\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><ol>\n<li>How many steps and replicas is sufficient for my peptide?\n<ul>\n<li>The longer the peptide is, the more difficult is the docking problem. We always suggest running more replicas with more steps if resource allow. A guideline should be running 100-300 replicas with a maximum Monte Carlo steps of\u00a0 1-3 million per amino acid in the peptide (10-30 million steps for a 10-mer peptide).<\/li>\n<\/ul>\n<\/li>\n<li>Do I start from a helix, an extended structure, or a mixture of both?\n<ul>\n<li>If you have prior knowledge of your peptide&#8217;s conformation. We suggest to start from that conformation. Starting from one conformation does not prevent the sampling of other conformation with different secondary structure. If nothing is known about the peptide, we suggest to start from a combination of 80% extended conformation and 20% helical conformation.<\/li>\n<\/ul>\n<\/li>\n<li>Why there are clashes in the output structure?\n<ul>\n<li>ADCP uses\u00a0 a discrete rotamer library to construct the sidechain and a coarse-grained scoring function for the internal energy. Thus, the output structure might have some minor clashes as well as nonoptimal bond angle and bond length. We suggest running a minimization with any MM force fields to resolve these minor issues. We will provide a all-in-one solution in the future.<\/li>\n<\/ul>\n<\/li>\n<li>Where are the caps at the peptide termini?\n<ul>\n<li>We discovered that there are different types of both peptide termini. We also found adding the proper caps does not conclusively help the docking. Thus, we decide to keep it simple by removing the caps while docking. Adding back the caps to the output structure can be done using software like VMD or PyMOL.<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/p>\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-223","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/223","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/comments?post=223"}],"version-history":[{"count":40,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/223\/revisions"}],"predecessor-version":[{"id":1171,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/223\/revisions\/1171"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/media?parent=223"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}