{"id":860,"date":"2019-04-17T18:30:21","date_gmt":"2019-04-17T18:30:21","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adfr\/?page_id=860"},"modified":"2019-10-30T22:36:59","modified_gmt":"2019-10-30T22:36:59","slug":"tutorial-redocking","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-redocking\/","title":{"rendered":"Tutorial redocking"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on October 30th, 2019 at 10:36 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>A simple re-docking tutorial<\/h3>\n<p>In this tutorial we illustrate how to re-dock a known ligand into its native receptor.\u00a0We will use the cyclic dependent kinase protein 2 CDK2 (pdbid:4EK3) and one of its ligands (pdbid:4EK4).<\/p>\n<p><strong>In this tutorial you will learn<\/strong>:<\/p>\n<ul>\n<li>to generate a target file for a docking in a box defined by the known ligand<\/li>\n<li>to run <em>ADFR<\/em> to re-dock the ligand<\/li>\n<li>to understand the output of an <em>ADFR<\/em> docking run<\/li>\n<\/ul>\n<\/div><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:25px;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-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-63671c38c2dda09fff5\" aria-selected=\"true\" id=\"fusion-tab-generatetargetfile\" href=\"#tab-63671c38c2dda09fff5\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate target file<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-9eba252d4a1d34f0ba4\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-inspecttargetfile\" href=\"#tab-9eba252d4a1d34f0ba4\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-search fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Inspect target file<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-2011278e0db8c4bf7de\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-dockingligand\" href=\"#tab-2011278e0db8c4bf7de\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking ligand<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-1fb0b448b5b2b6e8098\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-understandingtheoutput\" href=\"#tab-1fb0b448b5b2b6e8098\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-lightbulb far\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Understanding the output<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-ae92582ca4685bf7c0c\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-dockingmeta-data\" href=\"#tab-ae92582ca4685bf7c0c\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-search fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking meta-data<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-9ed7893786d681dbafa\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-exercise1:redocktheligand\" href=\"#tab-9ed7893786d681dbafa\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-question fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Exercise 1: redock the ligand<\/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-63671c38c2dda09fff5\" aria-selected=\"true\" id=\"mobile-fusion-tab-generatetargetfile\" href=\"#tab-63671c38c2dda09fff5\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate target file<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix in active\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-generatetargetfile\" id=\"tab-63671c38c2dda09fff5\">\n<h4>Generate the target file containing the affinity maps.<\/h4>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-1 > .CodeMirror, .fusion-syntax-highlighter-1 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-1 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_1\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_1\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_1\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">agfr -r data\/4EK3_rec.pdbqt -l data\/4EK4_lig.pdbqt -o ligPocket<\/textarea><\/div>\n<p>Alternatively, you can use <strong><em>agfrgui<\/em><\/strong> and follow the &#8220;<span id=\"sample-permalink\"><a href=\"https:\/\/ccsb.scripps.edu\/agfr\/boxligand\/\">https:\/\/ccsb.scripps.edu\/agfr\/<span id=\"editable-post-name\">boxligand<\/span><\/a><\/span>&#8221; tutorial<\/p>\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 <em>agfr<\/em>\u00a0is used to position and size the docking box over the receptor pocket(s) into which we want to dock a ligand, and compute affinity maps for a given list of <em>AutoDock4<\/em> atoms types. The maps are calculated by the <em>AutoGrid4<\/em>\u00a0program.<\/p>\n<p><strong>arguments<\/strong>:<\/p>\n<p>-r : specifies the receptor file<\/p>\n<p>-l : specifies the ligand file<\/p>\n<p>-o : specifies the name for the target files<\/p>\n<p>The receptor is specified using the <strong>\u2013r\/&#8211;receptor<\/strong> command line option. This option is required. The position and size of the box can be specified in a variety of ways using the <strong>\u2013b\/&#8211;boxMode<\/strong> option. In the example above,\u00a0<em>agfr<\/em>\u00a0creates the box as the bounding box of the given (known) ligand atoms (<strong>-l\/&#8211;ligand<\/strong>). By default, a padding of 4 \u00c5 is added to every side of the bounding box. The padding value can be modified using the <strong>\u2013P\/&#8211;padding<\/strong> option. is added on every side.<\/p>\n<p>The <em>agfr<\/em> command generates a target file with a .trg extension. This file will be saved under the name specified by the <strong>\u2013o\/&#8211;output<\/strong> command line option. When omitted, a unique and descriptive filename will be created automatically. The target file contains the calculated affinity maps, translational points for placing the ligand in sensible places in the docking box, and meta-data about the gird size, position, spacing, receptor atoms involved, affinity maps, etc. These files can be inspected using the <em>about<\/em> command.<\/p>\n<p>The translational points are computed using the <em>AutoSite<\/em>\u00a0program. This program will analyze affinity maps and cluster high affinity points to identify clusters of points modeling potential binding pockets. The <strong>\u2013p\/&#8211;pocketMode<\/strong> allows specifying how to handle multiple clusters of affinity points representing the pockets found in the docking box. Since this option is omitted here, all clusters are merged to create a single set of translational points.<\/p>\n<p>By default, maps are computed for all <em>AutoDock4<\/em> atom types. The list of atom types for which to compute affinity maps can be set using the <strong>\u2013m\/&#8211;mapTypes<\/strong> option. Generating affinity maps for fewer atom types generates smaller target files and takes less time to perform the calculation. However, such a target file cannot be used for docking ligands containing atoms for which the target files does not contain the affinity map.<\/p>\n<p>Running this command generates the following output (saved in ligPocket.log)<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-2 > .CodeMirror, .fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-2 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_2\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_2\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">MSMSLIB 1.4.4 started on fiji\nCopyright M.F. Sanner (March 2000)\nCompilation flags  \n#################################################################\n# If you used AGFR in your work, please cite:                   #\n#                                                               #\n# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #\n# M.F. Sanner                                                   #\n# AutoDockFR: Advances in Protein-Ligand Docking with           #\n# Explicitly Specified Binding Site Flexibility                 #\n# PLoS Comput Biol 11(12): e1004586                             #\n# DOI:10.1371\/journal.pcbi.1004586                              #\n#                                                               #\n# P. Ananad Ravindranath and M.F. Sanner                        #\n# AutoSite: an automated approach for pseudoligands prediction  #\n# - From ligand binding sites identification to predicting key  #\n# ligand atoms                                                  #\n# Bioinformatics (2016)                                         #\n# DOI:10.1093\/bioinformatics\/btw367                             #\n#                                                               #\n# Please see http:\/\/adfr.scripps.edu for more information.      #\n#################################################################\n\nComputing grids on fiji a Darwin-17.7.0-x86_64-i386-64bit computer\nDate Wed Apr 17 17:19:37 2019\n\nloading receptor: data\/4EK3_rec.pdbqt\nloading ligand: data\/4EK4_lig.pdbqt\n\nset box using ligand\n    Box center:    23.332    28.922    29.598\n    Box length:    17.250    16.500    12.000\n    Box size  :        46        44        32\n    padding   :     4.000\n    spacing   :     0.375\n\nidentifying pockets using AutoSite ....\n    found 4 pocket(s)\n\n    pocket|  energy | # of |Rad. of | energy |   bns    | score  \n    number|         |points|gyration|per vol.|buriedness|v*b^2\/rg\n    ------+---------+------+--------+--------+----------+---------\n        1   -120.94   267    4.12     -0.45      0.85      46.52\n        2    -20.77    32    2.20     -0.65      0.70       7.02\n        3     -8.36    12    1.25     -0.70      0.62       3.74\n        4     -8.27    14    1.17     -0.59      0.54       3.45\n    merging clusters ...\ndone. got 325 fill Points, in 0.59 (sec)\n\nsetting map types using: all to ['HS', 'Mg', 'HD', 'NA', 'Fe', 'Br', 'NS', 'A', 'C', 'Mn', 'G', 'F', 'I', 'H', 'J', 'N', 'Q', 'P', 'S', 'GA', 'Z', 'Zn', 'Cl', 'Ca', 'OA', 'SA', 'OS']\n\ncomputing maps for center=(23.332 28.922 29.598) size=(17.250 16.500 12.000) dims=(46 44 32) ...\n    320 points inside the box\n\n    maps computed in 3.32 (sec)\nAdding gradient to maps ...\nprocessing maps ... done 8.59889578819\nwriting maps ... done 1.53964877129\ndone adding gradient to maps 10.75 (sec)\nmaking target file ligPocket.trg ...done.\n    done. 15.51 (sec)\n<\/textarea><\/div>\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-9eba252d4a1d34f0ba4\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-inspecttargetfile\" href=\"#tab-9eba252d4a1d34f0ba4\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-search fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Inspect target file<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-inspecttargetfile\" id=\"tab-9eba252d4a1d34f0ba4\">\n<h4>Display information about a target file<\/h4>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-3 > .CodeMirror, .fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-3 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_3\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_3\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_3\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">about ligPocket.trg<\/textarea><\/div>\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 target file meta data is read and displayed.<\/p>\n<p>The command produces the following output:<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-4 > .CodeMirror, .fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-4 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_4\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_4\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-less\">docking target file\n  date       : Wed Apr 17 17:19:37 2019\n  node       : fiji\n  AGFR       : v1.2\n  AutoSite   : v1.0\n\n  receptor   : 4EK3_rec.pdbqt\n    FlexRec  : None\n    covBond  : No\n\n  box        :  mode ['ligand'], padding 4.00\n    center   : 23.332 28.922 29.598\n    length   : 17.250 16.500 12.000\n    size     : 0046 0044 0032\n    spacing  : 0.375\n\n  maps       : \n    types    :  C  GA  Fe   A   e   d   S   Q   F  SA   G   P  Mg  Cl  Zn  OA  NS  Ca  Br  Mn  OS  \n               NA   J   I  HS  HD   H   Z   N   W \n    W map    : weight 0.60 entropy -0.20\n    gradients: Yes,  kept largest negative cluster\n\n  pocketMode : ['ligand']\n    #fillpts : 320 points\n    file     : ligPocket\/translationPoints.npy\n<\/textarea><\/div>\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-2011278e0db8c4bf7de\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-dockingligand\" href=\"#tab-2011278e0db8c4bf7de\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking ligand<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-dockingligand\" id=\"tab-2011278e0db8c4bf7de\">\n<h3>Dock the randomized ligand using the generated target file<\/h3>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-5 > .CodeMirror, .fusion-syntax-highlighter-5 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-5 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_5\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_5\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_5\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"1\" data-theme=\"default\" data-mode=\"text\/x-sh\">adfr -l data\/4EK4_random.pdbqt -t ligPocket.trg --jobName rigid --nbRuns 8 --maxEvals 20000 -O --seed 1<\/textarea><\/div>\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:\u00a0<em>adfr<\/em> detects the number of cores available and by default will use them all to perform 8 independent searches (&#8211;<span class=\"SpellE\">nbRuns<\/span> 8) each using up to 200&#8217;000 evaluations of the scoring function (&#8211;<span class=\"SpellE\">maxEvals<\/span> 2000). By default <em>adfr<\/em> performs 50 searches, each allotted 2.5 million evaluations. Typically, more complex docking problems require more searches to be performed to increase the chances to find the best possible docked pose (i.e. global minimum of the scoring function). Here we set these parameters to lower values to perform a quick run that is sufficient to illustrate the docking principles.<\/p>\n<p>This calculation generates the following files:<\/p>\n<ul>\n<li>\n<pre>4EK4_random_rigid_summary.dlg\u00a0 \u00a0# the docking log file that captures most of what is displayed on the terminal<\/pre>\n<\/li>\n<li>\n<pre>4EK4_random_rigid_out.pdbqt\u00a0 \u00a0 \u00a0# the docking pose file containing the docking solutions<\/pre>\n<\/li>\n<li>\n<pre>4EK4_random_rigid.dro\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0# the docking object file that contains input, output, and meta-data for this docking run<\/pre>\n<\/li>\n<\/ul>\n<p>NOTES:<\/p>\n<ul>\n<li>The output files are named using\u00a0the ligand name followed by the job name (&#8211;<span class=\"SpellE\">jobName<\/span>\u00a0if specified)<\/li>\n<li>ADFR&#8217;s search procedure is stochastic, meaning that docking the same ligand into the same target twice can produce different results if\u00a0 different random number generator seeds are used. However, the energy landscape for this receptor and ligand is the same in both runs. If both docking runs find the global minimum of this energy landscape, the solutions produced by both runs will be the same, independently of the paths taken by the search to get there. On the other hand, searches that get trapped in a local minima, yield docking poses that differ from each other. Specifying the seeds used by the random number generator (&#8211;seed) allows reproducing a docking calculation, for a given version of the code.<\/li>\n<\/ul>\n<p>The output of the command is listed below:<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-6 > .CodeMirror, .fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-6 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_6\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_6\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"1\" data-theme=\"default\" data-mode=\"text\/x-less\">#################################################################\n# If you used ADFR in your work, please cite:                   #\n#                                                               #\n# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #\n# M.F. Sanner                                                   #\n#                                                               #\n# AutoDockFR: Advances in Protein-Ligand Docking with           #\n# Explicitly Specified Binding Site Flexibility                 #\n# PLoS Comput Biol 11(12): e1004586                             #\n#                                                               #\n# DOI:10.1371\/journal.pcbi.1004586                              #\n#                                                               #\n# Please see http:\/\/adfr.scripps.edu for more information.      #\n#################################################################\n\nDocking on fiji a Darwin-17.7.0-x86_64-i386-64bit computer\nDate Thu Apr 18 09:11:45 2019\nreading ligand \/Users\/sanner\/test1.1\/data\/4EK4_random.pdbqt\nDetected 4 cores, using 4 cores\nUnpacking maps \/Users\/sanner\/test1.1\/ligPocket.trg\nPerforming search (8 GA evolutions with 20000 maxEvals each) ...\n0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\nTermination status\n    0\/   8  0.0% runs failed\n    8\/   8 100.0% runs exhausted their evaluations\n    0\/   8  0.0% runs stopped converged 1 or 2 clusters\n    0\/   8  0.0% runs stopped after no improvement in clusters\n    0\/   8  0.0% runs stopped because GA ran out of choices\n    0\/   8  0.0% runs stopped because GA population converged\n\nRefining results ...\ndone.\n\nmode |  affinity  | clust. | ref. | clust. | rmsd | energy | best |\n     | (kcal\/mol) | rmsd   | rmsd |  size  | stdv |  stdv  | run  |\n-----+------------+--------+------+--------+------+--------+------+\n   1         -7.0     0.0    -1.0       4     0.4     0.2    004\n   2         -6.3     5.0    -1.0       3     0.6     0.1    003\n   3         -6.1     2.0    -1.0       1      NA      NA    006\nWriting poses to 4EK4_random_rigid_out.pdbqt\n\nDocking performed in 7.17 seconds, i.e. 0 hours 00 minutes 07.170796 seconds \n\n*************** first GA command ***************************\n\"\/Users\/sanner\/test1.1\/mgltools2_x86_64Darwin_1.2\/bin\/pythonsh\" \"\/Users\/sanner\/test1.1\/ADFR\/bin\/runOneGA.py\" -F \"\/var\/folders\/gm\/frz8gxj57hzbyyzwtt5bq8m40000gn\/T\/tmp99PZpp\/ligPocket\" -M rigidReceptor -R \"\/var\/folders\/gm\/frz8gxj57hzbyyzwtt5bq8m40000gn\/T\/tmp99PZpp\/ligPocket\/4EK3_rec.pdbqt\" -T \"\/var\/folders\/gm\/frz8gxj57hzbyyzwtt5bq8m40000gn\/T\/tmp99PZpp\/ligPocket\/translationPoints.npy\" \"-l\" \"data\/4EK4_random.pdbqt\" \"--jobName\" \"rigid\" \"--maxEvals\" \"20000\" \"-O\" -S 1 -j 1 -o \"4EK4_random_rigid\/rigid0001.dlg\"\n\npackaging docking results in to 4EK4_random_rigid.droin  0.12 (s.)\n<\/textarea><\/div>\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-1fb0b448b5b2b6e8098\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-understandingtheoutput\" href=\"#tab-1fb0b448b5b2b6e8098\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-lightbulb far\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Understanding the output<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-understandingtheoutput\" id=\"tab-1fb0b448b5b2b6e8098\">\n<p>Here we describe line by line the messages output during the docking procedure.<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-7 > .CodeMirror, .fusion-syntax-highlighter-7 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-7 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-7 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-7 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_7\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_7\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-less\">Docking on fiji a Darwin-17.7.0-x86_64-i386-64bit computer\nDate Wed Apr 17 13:12:08 2019\nreading ligand \/Users\/sanner\/test1.1\/data\/4EK4_lig.pdbqt\nDetected 4 cores, using 4 cores\nUnpacking maps \/Users\/sanner\/test1.1\/4ek3_rec.trg\nreading reference ligand \/Users\/sanner\/test1.1\/data\/4EK4_lig.pdbqt\n<\/textarea><\/div>\n<ol>\n<li>Hostname and platform architecture on which the program is running<\/li>\n<li>Date and time of execution<\/li>\n<li>ligand docked<\/li>\n<li>number of detected and used cores.<\/li>\n<li>target files used<\/li>\n<li>Reference ligand used<\/li>\n<\/ol>\n<p>NOTES:<\/p>\n<ul>\n<li>Number of cores. By default ADFR will use all cores available to parallelize the search threads comprised in a run. Use the &#8220;-c&#8221; command line option to limit the number of used cores.<\/li>\n<li>Reference ligand. It is not uncommon to start a docking project by re-docking a known ligand to gain confidence that the docking process is working for this complex. In such a case specifying a reference ligand allows estimation of success as the RMSD of the docked poses to the reference will be listed in the output.<\/li>\n<\/ul>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-8 > .CodeMirror, .fusion-syntax-highlighter-8 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-8 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-8 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-8 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_8\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_8\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">Performing search (8 GA evolutions with 20000 maxEvals each) ...\n0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\nTermination status\n    0\/   8  0.0% runs failed\n    8\/   8 100.0% runs exhausted their evaluations\n    0\/   8  0.0% runs stopped converged 1 or 2 clusters\n    0\/   8  0.0% runs stopped after no improvement in clusters\n    0\/   8  0.0% runs stopped because GA ran out of choices\n    0\/   8  0.0% runs stopped because GA population converged\n<\/textarea><\/div>\n<p>By default, ADFR performs 50 independent searches, i.e. 50 evolutions of a population of 100 individuals using a Genetic Algorithm (GA). In this example we intentionally reduced this number to 8 very short runs.<\/p>\n<p>Lines 1-4 display a progress bar indicating the percentage of these runs that completed.<\/p>\n<p>The lines below provide statistics over the termination status of these searches. <em>ADFR<\/em>\u00a0implements several termination criteria in its search method. In this example all search terminated because they reached their maximum number of evaluations. The default number of evaluations is 2.5 millions and is usually never reached because of other termination criteria such as convergence of the population, meaning that there is no more diversity in the population and the chances to discover new solutions has become small, or the population still has diversity (i.e. it contains multiples competitive solutions) but none of these solution has improves over a user-defined number of generations (default 5).<\/p>\n<p>Typically, you want searches to end because the population converged or there was no improvement. A result like the one shown here is a clear indication that this docking problem needs more evaluations per search (i.e. increased &#8211;maxEvals).<\/p>\n<p>The next section lists the results:<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-9 > .CodeMirror, .fusion-syntax-highlighter-9 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-9 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-9 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-9 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_9\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_9\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-less\">Refining results ...\ndone.\n\nmode |  affinity  | clust. | ref. | clust. | rmsd | energy | best |\n     | (kcal\/mol) | rmsd   | rmsd |  size  | stdv |  stdv  | run  |\n-----+------------+--------+------+--------+------+--------+------+\n   1         -7.0     0.0    -1.0       4     0.4     0.2    004\n   2         -6.3     5.0    -1.0       3     0.6     0.1    003\n   3         -6.1     2.0    -1.0       1      NA      NA    006\n<\/textarea><\/div>\n<p>In this docking run, the 8 searches lead to 3 distinct solutions, listed in the result table above. The solutions are sorted by descending predicted affinity. The top ranking solution was identified by 4 of the 8 searches (<em>clust. size<\/em> column) and the pose with the best affinity was found by search number 4 (<em>best run<\/em> column). The second best solution was found 3 times and the best pose in this cluster of 3 search results has an RMSD of 5.0 Angstroms with the top ranking solution (<em>clust. rmsd<\/em> column). If a reference ligand pose had been specified (-r\/referenceLigand option), The <em>ref. rmsd<\/em> column would list the RMSD between the docked pose and the reference structure instead of listing -1.<\/p>\n<p>NOTE: RMSD values are calculated using all isomorphisms\u00a0 between the 2 molecules, thus matching symmetry related atoms and providing a more accurate measure that used in <em>AutoDock4<\/em>, <em>Vina<\/em>, and previous versions of <em>AutoDockFR<\/em>.<\/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-ae92582ca4685bf7c0c\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-dockingmeta-data\" href=\"#tab-ae92582ca4685bf7c0c\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-search fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking meta-data<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-dockingmeta-data\" id=\"tab-ae92582ca4685bf7c0c\">\n<h4>Display information about a docking result<\/h4>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-10 > .CodeMirror, .fusion-syntax-highlighter-10 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-10 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_10\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_10\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_10\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">about 4EK4_random_rigid.dro<\/textarea><\/div>\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 meta data about this docking run is displayed<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-11 > .CodeMirror, .fusion-syntax-highlighter-11 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-11 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-11 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-11 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_11\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_11\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">docking result file\n  date       : Thu Apr 18 09:11:45 2019\n  node       : fiji\n  platform   : Darwin-17.7.0-x86_64-i386-64bit\n  ncores     : 4\n\n  receptor   : ligPocket.trg\n   docking target file\n     date       : Thu Apr 18 09:08:42 2019\n     node       : fiji\n     AGFR       : v1.2\n     AutoSite   : v1.0\n\n     receptor   : 4EK3_rec.pdbqt\n       FlexRec  : None\n       covBond  : No\n\n     box        :  mode ['ligand'], padding 4.00\n       center   : 23.332 28.922 29.598\n       length   : 17.250 16.500 12.000\n       size     : 0046 0044 0032\n       spacing  : 0.375\n\n     maps       : \n       types    :  C  GA  Fe   A   e   d   S   Q   F  SA   G   P  Mg  Cl  Zn  OA  NS  Ca  Br  Mn  OS  \n                  NA   J   I  HS  HD   H   Z   N   W \n       W map    : weight 0.60 entropy -0.20\n       gradients: Yes,  kept largest negative cluster\n\n     pocketMode : ['ligand']\n       #fillpts : 320 points\n       file     : ligPocket\/translationPoints.npy\n\n  ligand     : 4EK4_random.pdbqt\n     nbAtoms : 18\n     types   : A:9 C:2 NA:1 OA:1 N:2 Br:1 HD:2 \n  lig ref    : None\n  summary    : 4EK4_random_rigid_summary.dlg\n  GA params  : \n    maxEvals : 20000\n    nbRuns   : 8\n    jobName  : rigid\n    seed     : 1\n    covLig   : None\n<\/textarea><\/div>\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-9ed7893786d681dbafa\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-exercise1:redocktheligand\" href=\"#tab-9ed7893786d681dbafa\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-question fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Exercise 1: redock the ligand<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-exercise1:redocktheligand\" id=\"tab-9ed7893786d681dbafa\">\n<p>the command<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-12 > .CodeMirror, .fusion-syntax-highlighter-12 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-12 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_12\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_12\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_12\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"1\" data-theme=\"default\" data-mode=\"text\/x-sh\">adfr -l data\/4EK4_random.pdbqt -t ligPocket.trg --jobName rigid --nbRuns 8 --maxEvals 20000 -O --seed 1<\/textarea><\/div>\n<p>leads to 3 distinct solutions. Can you modify the command to re-dock the randomized ligand in crystallographic pose reliably?<\/p>\n<p>The crystal structure of the ligand is in data\/4EK4_lig.pdbqt<\/p>\n<p><a href=\"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-_redockingex1\/\" target=\"_blank\" rel=\"noopener\">ANSWER<\/a><\/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 October 30th, 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-860","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/860","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=860"}],"version-history":[{"count":40,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/860\/revisions"}],"predecessor-version":[{"id":1123,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/860\/revisions\/1123"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/media?parent=860"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}