{"id":559,"date":"2019-04-13T00:47:46","date_gmt":"2019-04-13T00:47:46","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/agfr\/?page_id=559"},"modified":"2019-05-15T22:20:06","modified_gmt":"2019-05-15T22:20:06","slug":"flexible-receptor-sidechains","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/agfr\/flexible-receptor-sidechains\/","title":{"rendered":"Flexible Receptor Sidechains"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on May 15th, 2019 at 10:20 pm<\/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;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h3>Use case 4: docking with flexible receptor side chains<\/h3>\n<p>In this scenario we have a receptor and a known ligand available in the PDBQT format and we define a docking box centered on the ligand.<\/p>\n<p>We will use the cyclic dependent kinase protein 2 CDK2 (pdbid:4EK3) and ligands (pdbid:1YKR). The files 4EK3_rec.pdbqt and 1YKR_lig.pdbqt are available in the <a href=\"https:\/\/ccsb.scripps.edu\/adfr\/download\/1063\/\">data file associated with this tutorial<\/a>.<\/p>\n<p>run\u00a0<em><strong>ADFRsuite-1.0\/bin\/agfrgui<\/strong><\/em>\u00a0to start the Graphical User interface for these tutorials.<\/p>\n<\/div><div class=\"fusion-tabs fusion-tabs-1 clean vertical-tabs icon-position-left mobile-mode-accordion\" style=\"--awb-title-border-radius-top-left:0px;--awb-title-border-radius-top-right:0px;--awb-title-border-radius-bottom-right:0px;--awb-title-border-radius-bottom-left:0px;--awb-inactive-color:#9acae0;--awb-background-color:#ffffff;--awb-border-color:#9acae0;--awb-active-border-color:#d65169;\"><div class=\"nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li class=\"active\" role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-342f13a3d2fcdb2cecb\" aria-selected=\"true\" id=\"fusion-tab-loadreceptor\" href=\"#tab-342f13a3d2fcdb2cecb\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-keyboard fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Load receptor<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-c81a0e4b84bed590132\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-loadligand\" href=\"#tab-c81a0e4b84bed590132\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-keyboard fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Load ligand<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-f5baed730bc958dc913\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-definebox\" href=\"#tab-f5baed730bc958dc913\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Define box<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-7fcfaf391033c4ea628\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-makesidechainsflexible\" href=\"#tab-7fcfaf391033c4ea628\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Make side chains flexible<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-e7145c4fca1a781d32e\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-moreflexibleresidues\" href=\"#tab-e7145c4fca1a781d32e\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>More flexible residues<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-132c2ebaf0485752638\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-adjustthebox\" href=\"#tab-132c2ebaf0485752638\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Adjust the box<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-7b12f767fd12ecdd77e\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-bindingpockets\" href=\"#tab-7b12f767fd12ecdd77e\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Binding pockets<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-ed091947a3bf3ee9a78\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-mapsparameters\" href=\"#tab-ed091947a3bf3ee9a78\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Maps parameters<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-1765a5c64e06ffb9231\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-generatemaps\" href=\"#tab-1765a5c64e06ffb9231\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-calculator fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate maps<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-content\"><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li class=\"active\" role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-342f13a3d2fcdb2cecb\" aria-selected=\"true\" id=\"mobile-fusion-tab-loadreceptor\" href=\"#tab-342f13a3d2fcdb2cecb\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-keyboard fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Load receptor<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix in active\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-loadreceptor\" id=\"tab-342f13a3d2fcdb2cecb\">\n<h4><span style=\"color: #008080;\">Click\u00a0<img decoding=\"async\" class=\"wp-image-743 alignnone\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-8.50.57-AM.png\" alt=\"\" width=\"96\" height=\"40\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-8.50.57-AM-200x83.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-8.50.57-AM.png 226w\" sizes=\"(max-width: 96px) 100vw, 96px\" \/> and select 4EK3_rec.pdbqt<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: the receptor molecule is loaded and displayed as line representing atomic bonds colored by atom type with carbon atoms shown in cyan. The default docking-box covers the entire receptor with the default padding (4.0 Angstroms) added to each side.<\/p>\n<p><img decoding=\"async\" width=\"995\" height=\"770\" class=\"wp-image-508 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1.png\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-200x155.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-300x232.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-400x310.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-600x464.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-768x594.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1-800x619.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1.png 995w\" sizes=\"(max-width: 995px) 100vw, 995px\" \/><\/p>\n<p>NOTES:<\/p>\n<ul>\n<li>Amino acids located in the docking box with no flexible side-chains (<em>i.e.<\/em> glycine, alanine and proline) are displayed with dimmed down lines.<\/li>\n<li>Several buttons in the control section and the tool-bar are now enabled.<\/li>\n<li>The status bar indicates that the next step could be to detect pockets.<\/li>\n<\/ul>\n<p>The 3D scene can be rotated, translated and scaled using the 3 mouse buttons:<\/p>\n<div class=\"table-1\">\n<table style=\"height: 142px;\" width=\"251\">\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Mouse button<\/td>\n<td style=\"text-align: left;\">Action<\/td>\n<\/tr>\n<tr>\n<td>Left<\/td>\n<td>Rotate<\/td>\n<\/tr>\n<tr>\n<td>Middle<\/td>\n<td>Translate<\/td>\n<\/tr>\n<tr>\n<td>Right<\/td>\n<td>Scale<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p>Depth-cueing can be turned on and off by pressing the keyboard key \u2018d\u2019 while the mouse pointer is in the 3D view.<\/p>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-c81a0e4b84bed590132\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-loadligand\" href=\"#tab-c81a0e4b84bed590132\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-keyboard fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Load ligand<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-loadligand\" id=\"tab-c81a0e4b84bed590132\">\n<h4><span style=\"color: #008080;\">Click on the <img decoding=\"async\" class=\"wp-image-509\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-2.png\" width=\"80\" height=\"46\" \/> button to load 1YKR_lig.pdbqt<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: the ligand molecule appears in the licorice representation with carbon atoms displayed in yellow.<\/p>\n<p><img decoding=\"async\" class=\"alignleft size-full wp-image-792\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM.png\" alt=\"\" width=\"2134\" height=\"1652\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-200x155.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-300x232.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-400x310.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-600x464.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-768x595.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-800x619.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-1024x793.png 1024w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM-1200x929.png 1200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.08.46-PM.png 2134w\" sizes=\"(max-width: 2134px) 100vw, 2134px\" \/><\/p>\n<p>NOTE:<\/p>\n<ul>\n<li>More buttons are enabled by this operation both in the control panel and in the tool-bar. In particular the button allowing to position and size the box using the ligand\u00a0<img decoding=\"async\" class=\"size-full wp-image-655 alignnone\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-57.png\" alt=\"\" width=\"47\" height=\"47\" \/>.<\/li>\n<\/ul>\n<h2><\/h2>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-f5baed730bc958dc913\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-definebox\" href=\"#tab-f5baed730bc958dc913\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Define box<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-definebox\" id=\"tab-f5baed730bc958dc913\">\n<h4><span style=\"color: #008080;\">Click\u00a0\u00a0<img decoding=\"async\" width=\"47\" height=\"47\" class=\"wp-image-512\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-5.png\" \/>\u00a0to make the docking box cover the ligand, click on <img decoding=\"async\" width=\"42\" height=\"40\" class=\"wp-image-513\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-6.png\" \/> to focus the 3D scene on the box, and click<img decoding=\"async\" class=\"wp-image-566\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-16.png\" width=\"29\" height=\"28\" \/>\u00a0to label residues in the box.<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: the docking box is now centered on the ligand and scaled to have a 4.0 angstroms padding from the ligand atoms.<\/p>\n<p>The padding can be adjusted using the spin box in the \u201cdocking box\u201d section.<\/p>\n<p><img decoding=\"async\" class=\"alignleft size-full wp-image-565\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15.png\" alt=\"\" width=\"1024\" height=\"739\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-200x144.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-300x217.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-400x289.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-600x433.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-768x554.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15-800x577.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-15.png 1024w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/><\/p>\n<p>This particular ligand overlaps with side chains of the receptor\u2019s apo conformation. Label the receptor residues in the docking box by clicking in the\u00a0<img decoding=\"async\" class=\"wp-image-566\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-16.png\" width=\"29\" height=\"28\" \/>\u00a0button in the tool bar, and zoom in and rotate to observe the overlap of lysine 33 and lysine 89 with the ligand.<img decoding=\"async\" class=\"wp-image-564 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image.jpeg\" alt=\"\" width=\"710\" height=\"532\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-200x150.jpeg 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-300x225.jpeg 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-400x300.jpeg 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-600x450.jpeg 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-768x576.jpeg 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-800x600.jpeg 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1024x768.jpeg 1024w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1200x900.jpeg 1200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image.jpeg 1280w\" sizes=\"(max-width: 710px) 100vw, 710px\" \/><\/p>\n<p>NOTES:<\/p>\n<ul>\n<li>It is recommended to keep the number of flexible receptor side chains below 15.<\/li>\n<\/ul>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-7fcfaf391033c4ea628\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-makesidechainsflexible\" href=\"#tab-7fcfaf391033c4ea628\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Make side chains flexible<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-makesidechainsflexible\" id=\"tab-7fcfaf391033c4ea628\">\n<h4><span style=\"color: #008080;\">Click on <img decoding=\"async\" class=\"size-full wp-image-567 alignnone\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-17.png\" alt=\"\" width=\"55\" height=\"27\" \/>\u00a0and select LYS33 and LYS89<br \/>\n<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: a residue selection widget displays all receptor amino acids currently in the docking box and having a side chain that can adopt multiple conformations (<em>i.e.<\/em>\u00a0not alanine, glycine or proline). Check the box for a residue select it for having its side chain made flexible during the docking. Side chains selected as flexible for docking are displayed in the 3D view as orange Sticks &amp; Balls and listed in the type in widget.<\/p>\n<p><img decoding=\"async\" class=\"size-full wp-image-568 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18.png\" alt=\"\" width=\"729\" height=\"545\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-200x150.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-300x224.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-400x299.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-600x449.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18.png 729w\" sizes=\"(max-width: 729px) 100vw, 729px\" \/><\/p>\n<p>NOTES:<\/p>\n<ul>\n<li>If a ligand has been loaded, receptor side chains to be made flexible can also be selected based on their distance from the ligand by checking the \u201cresidue within\u201d button. Checking this button will override the current selection with the set of receptor side chains having at least one moving side chain atom within the current distance cutoff (i.e. 3.0 Angstroms in this case) of the ligand. Keep in mind that the more side chains are made flexible the harder the docking problem. While <em>ADFR<\/em> has no hard limit on how many side-chains can be made flexible we recommend keeping the number below 10\u00a0 to 15.<\/li>\n<li>The receptor amino acids selected to have flexible side-chains during the docking calculation are now listed in the type-in widget.\u00a0<img decoding=\"async\" width=\"140\" height=\"56\" class=\"wp-image-569 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-19.png\" \/>\u00a0along with the number such residues. Flexible residues can be specified manually by typing directly in this widget. A residue can be specified by its residue number (<em>e.g.<\/em>\u00a0\u201c89\u201d), or by its residue type and number (<em>e.g.<\/em>\u201cLYS89\u201d). Multiple residues must be separated by a comma \u2018,\u2019 or space characters, optionally preceded by a chain id (i.e. \u201cA:120,LYS89\u201d). If the chain id is omitted matching residues from all chains are selected. Residues from different chains can be specified by separating the selection string for each chain by a semi colon \u2018;\u2019\u00a0<em>e.g.<\/em>\u00a0\u201cA:10,24,35;B:12,34\u201d<\/li>\n<li>Close the interface by destroying the window, using the button in the corner of the window.<\/li>\n<\/ul>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-e7145c4fca1a781d32e\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-moreflexibleresidues\" href=\"#tab-e7145c4fca1a781d32e\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>More flexible residues<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-moreflexibleresidues\" id=\"tab-e7145c4fca1a781d32e\">\n<h4><span style=\"color: #008080;\">Type &#8220;,88&#8221; in the type-in widget for flexible residues en press the key<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details:<\/p>\n<ul>\n<li>one more residue (lysine 88) is selected to be have a flexible side chain during docking.<\/li>\n<li>the flexible residues and the selection string in expanded.<\/li>\n<li>the &#8216;FR&#8217; status light (bottom right of the GUI) turned red (i.e. invalid box)<\/li>\n<\/ul>\n<p><img decoding=\"async\" class=\"size-full wp-image-570 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-20.png\" alt=\"\" width=\"592\" height=\"489\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-20-200x165.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-20-300x248.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-20-400x330.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-20.png 592w\" sizes=\"(max-width: 592px) 100vw, 592px\" \/><\/p>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-132c2ebaf0485752638\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-adjustthebox\" href=\"#tab-132c2ebaf0485752638\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Adjust the box<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-adjustthebox\" id=\"tab-132c2ebaf0485752638\">\n<h4><span style=\"color: #008080;\">Click on\u00a0<img decoding=\"async\" width=\"56\" height=\"27\" class=\"wp-image-571\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-21.png\" \/>\u00a0to adjust the docking box to cover all flexible receptor atoms<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details:<\/p>\n<ul>\n<li>the docking box has been extended to fully cover all flexible residues (33, 88 and 89)<\/li>\n<li>the status light for flexible receptor side chains validity \u2018FR\u2019 is now green in the status bar<\/li>\n<\/ul>\n<p><img decoding=\"async\" width=\"803\" height=\"621\" class=\"wp-image-572 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22.png\" sizes=\"(max-width: 803px) 100vw, 803px\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-200x155.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-300x232.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-400x309.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-600x464.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-768x594.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22-800x619.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-22.png 803w\" \/><\/p>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-7b12f767fd12ecdd77e\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-bindingpockets\" href=\"#tab-7b12f767fd12ecdd77e\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Binding pockets<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-bindingpockets\" id=\"tab-7b12f767fd12ecdd77e\">\n<h4><span style=\"color: #008080;\">Click on\u00a0<img decoding=\"async\" class=\" wp-image-755 alignnone\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM.png\" sizes=\"(max-width: 254px) 100vw, 254px\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM-200x19.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM-300x28.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM-400x38.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM-540x52.png 540w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM.png 550w\" alt=\"\" width=\"254\" height=\"24\" \/><\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: ligand binding pockets are computed using <a href=\"http:\/\/adfr.scripps.edu\/autosite\"><em>AutoSite<\/em><\/a>\u00a0by identifying and cluster high affinity points. Each cluster of points is called a &#8220;fill&#8221; and listed in the table widget. The pocket with the largest <em>AutoSite<\/em> score is selected by defaults and displayed as a set of green dots. The fill points of all selected fills are displayed in the 3D viewer and will be written into the target files.<\/p>\n<p>NOTES:<\/p>\n<ul>\n<li>the &#8220;Pocket&#8221; status light is now green<\/li>\n<li>the &#8220;generate target file &#8230;&#8221; is enabled.<\/li>\n<\/ul>\n<p><img decoding=\"async\" class=\"alignleft size-full wp-image-794\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM.png\" alt=\"\" width=\"2664\" height=\"1652\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-200x124.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-300x186.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-400x248.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-600x372.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-768x476.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-800x496.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-1024x635.png 1024w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM-1200x744.png 1200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.57.15-PM.png 2664w\" sizes=\"(max-width: 2664px) 100vw, 2664px\" \/><\/p>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-ed091947a3bf3ee9a78\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-mapsparameters\" href=\"#tab-ed091947a3bf3ee9a78\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-filter fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Maps parameters<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-mapsparameters\" id=\"tab-ed091947a3bf3ee9a78\">\n<h4><span style=\"color: #008080;\">Check the\u00a0<img decoding=\"async\" class=\" wp-image-760 alignnone\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.18.49-AM.png\" alt=\"\" width=\"145\" height=\"34\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.18.49-AM-200x47.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.18.49-AM.png 264w\" sizes=\"(max-width: 145px) 100vw, 145px\" \/> button<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details:\u00a0loading the ligand initialized the list of maps to be computed to the list of <em>AutoDock<\/em> atom types found in the ligand, in this case: \u201cA C Cl HD N NA OA\u201d.\u00a0Computing maps for all atoms types will use a little more disk space but the resulting target file can be used for any ligand and is recommended.<\/p>\n<p><img decoding=\"async\" class=\" wp-image-758 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM.png\" alt=\"\" width=\"513\" height=\"315\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM-200x123.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM-300x184.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM-400x246.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM-600x369.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM-768x472.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM.png 784w\" sizes=\"(max-width: 513px) 100vw, 513px\" \/><\/p>\n<p>The \u201cedit \u2026\u201d button will display an interface for manually specifying the list of atoms types for which affinity maps are requested.<\/p>\n<p><strong>Water maps<\/strong>: water maps\u00a0 are calculated automatically and stored in the target file. These maps allow to perform <a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/jm2005145\">hydrated docking<\/a>. the parameter for these maps can be set in the &#8220;water map setting&#8221; pull down.<\/p>\n<p><img decoding=\"async\" class=\" wp-image-759 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.17.06-AM.png\" alt=\"\" width=\"162\" height=\"110\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.17.06-AM-200x136.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.17.06-AM-300x204.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.17.06-AM.png 350w\" sizes=\"(max-width: 162px) 100vw, 162px\" \/><\/p>\n<p><strong>Gradients<\/strong>: By default, an affinity gradient will be created for the region of the grid covered by the receptor (except for the electrostatic and desolvation maps). If your CPU has multiple cores and OpenMP is detected, the calculation will execute in parallel and the number of available threads appears in the GUI title bar. Gradients are not required, however, they are recommended as they have been shown to\u00a0help docking find solutions more efficiently. The addition of gradients requires the definition of the <em>interior<\/em> and <em>exterior<\/em> of the receptor. By default, the largest cluster of negative values (favorable affinities) is used to define the exterior of the receptor. In this case, everything else, including receptor cavities large enough to hold solvent but not open to the solvent, will be considered the interior and will be overwritten with the gradient. To prevent the gradient generation on grid points of internal cavities, the user can specify a cluster size above which clusters of points with negative values are considered to be outside the receptor and therefore preserve their original affinity values.<\/p>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-1765a5c64e06ffb9231\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-generatemaps\" href=\"#tab-1765a5c64e06ffb9231\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-calculator fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate maps<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-generatemaps\" id=\"tab-1765a5c64e06ffb9231\">\n<h4><span style=\"color: #008080;\">Click on the \u201cgenerate target file\u2026\u201d button, name the target file as\u00a04EK3_FR33_88_89\u00a0<\/span><\/h4>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Details: the program asks for the name and location for the target file that will be generated. It will then compute the affinity maps and store them in the target file along with meta data.<\/p>\n<p><img decoding=\"async\" class=\"wp-image-795 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM.png\" alt=\"\" width=\"441\" height=\"265\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-200x120.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-300x181.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-400x241.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-600x361.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-768x462.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM-800x481.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-2.59.33-PM.png 924w\" sizes=\"(max-width: 441px) 100vw, 441px\" \/><\/p>\n<p>The generated target file describes the binding pocket targeted for docking on the receptor. It stores the PDBQT file of the receptor used to compute the affinity maps, the grid parameter file used to run <em>AutoGrid,<\/em> as well as files generated by the <em>AutoGrid<\/em>\u00a0run (<em>i.e.<\/em> affinity maps, <em>AutoGrid<\/em> log file, etc.). In addition, it stores meta-data about the generation of the target file such as: the time and computer architecture on which the maps were computed, the docking-box parameters, the grid parameter file, the versions of <em>AGFR<\/em> and\u00a0<em>AutoSite<\/em>, the water map parameters, etc.<\/p>\n<p>It is recommended to use names that are descriptive. In this case we use\u00a04EK3_FR33_88_89.<\/p>\n<p>Pressing the \u201cSave\u201d button will start the calculation in a separate thread, leaving the graphical user interface responsive. The progress bar below the button will indicate the level of completion of the calculation.<\/p>\n<p><img decoding=\"async\" class=\" wp-image-764 aligncenter\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM.png\" alt=\"\" width=\"323\" height=\"71\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM-200x44.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM-300x66.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM-400x88.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM-600x132.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM-768x169.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM.png 792w\" sizes=\"(max-width: 323px) 100vw, 323px\" \/><\/p>\n<p>NOTE: a target file can be inspected from the command line using the <em>about<\/em> command (<em>AutoDockSuite-1.0\/bin\/about<\/em>)<\/p>\n<\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>This page was last updated on May 15th, 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-559","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/559","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/comments?post=559"}],"version-history":[{"count":9,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/559\/revisions"}],"predecessor-version":[{"id":892,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/559\/revisions\/892"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/media?parent=559"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}