{"id":273,"date":"2021-10-26T16:07:14","date_gmt":"2021-10-26T16:07:14","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/autosite\/?page_id=273"},"modified":"2021-10-26T19:05:01","modified_gmt":"2021-10-26T19:05:01","slug":"smallmoleculeastutorial1","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/autosite\/smallmoleculeastutorial1\/","title":{"rendered":"smallMoleculeAStutorial1"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 fusion-flex-container 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 fusion-flex-align-items-flex-start fusion-flex-content-wrap\" style=\"max-width:2288px;margin-left: calc(-4% \/ 2 );margin-right: calc(-4% \/ 2 );\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-flex-column\" style=\"--awb-bg-size:cover;--awb-width-large:100%;--awb-margin-top-large:0px;--awb-spacing-right-large:1.92%;--awb-margin-bottom-large:20px;--awb-spacing-left-large:1.92%;--awb-width-medium:100%;--awb-order-medium:0;--awb-spacing-right-medium:1.92%;--awb-spacing-left-medium:1.92%;--awb-width-small:100%;--awb-order-small:0;--awb-spacing-right-small:1.92%;--awb-spacing-left-small:1.92%;\"><div class=\"fusion-column-wrapper fusion-column-has-shadow fusion-flex-justify-content-flex-start fusion-content-layout-column\"><div class=\"fusion-text fusion-text-1\"><h3>A simple AutoSite tutorial<\/h3>\n<p>In this tutorial we illustrate how to identify binding pockets in the biotin binding protein (PDBID: 1STP).<\/p>\n<p><strong>In this tutorial you will learn<\/strong>:<\/p>\n<ul>\n<li>to run AutoSite for a macromolecule<\/li>\n<li>to locate and understand the various output file generated by AutoSite.<\/li>\n<\/ul>\n<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\/autosite\/wp-content\/uploads\/sites\/50\/2021\/10\/1STP.tgz\">data file associated with this tutorial<\/a>.<\/li>\n<\/ul>\n<h2>Go back to <a href=\"https:\/\/ccsb.scripps.edu\/autosite\/\">AutoSite Homepage<\/a>.<\/h2>\n<\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"align-self: center;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-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:#ba43a6;\"><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-14c540697ba61d2b068\" aria-selected=\"true\" id=\"fusion-tab-runautosite\" href=\"#tab-14c540697ba61d2b068\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Run AutoSite<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-d48a33c77bafc5f0084\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-outputfiles\" href=\"#tab-d48a33c77bafc5f0084\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-lightbulb fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Output files<\/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-14c540697ba61d2b068\" aria-selected=\"true\" id=\"mobile-fusion-tab-runautosite\" href=\"#tab-14c540697ba61d2b068\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Run AutoSite<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix in active\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-runautosite\" id=\"tab-14c540697ba61d2b068\">\n<p>AutoSite requires the macro-molecule to be provided in the PDBQT format. the input file 1STP.pdbqt can be downloaded <a href=\"https:\/\/ccsb.scripps.edu\/autosite\/wp-content\/uploads\/sites\/50\/2021\/10\/1STP.tgz\">here<\/a> (tar zxvf 1STP.tgz).<\/p>\n<pre>&gt; autosite -r 1STP.pdbqt<\/pre>\n<p>this command will generate the following output<\/p>\n<pre>#################################################################\r\n# If you used AutoSite in your work, please cite:               #\r\n#                                                               #\r\n# Pradeep Anand Ravindranath and Michel F. Sanner               #\r\n#                                                               #\r\n# AutoSite: an automated approach for pseudoligands             #\r\n# prediction - From ligand binding sites identification to      #\r\n# predicting key ligand atoms                                   #\r\n#                                                               #\r\n# Bioinformatics (2016)                                         #\r\n#                                                               #\r\n# DOI: 10.1093\/bioinformatics\/btw367                            #\r\n#                                                               #\r\n# Please see http:\/\/adfr.scripps.edu\/AutoDockFR\/autosite.html   #\r\n# for more information                                          #\r\n#################################################################\r\nAutoSite v1.0.0 started on a Linux-5.11.0-38-generic-x86_64-with-debian-bullseye-sid computer Date Tue Oct 26 10:37:19 2021 computing maps .... No cutoff scan and use cutoffs -0.3 -0.66 -0.5 clustering high affinity points ... analysing 4 clusters ... saving 4 clusters and associated feature points in folder 1STP\r\n\r\nclust.| Energy| # of |Rad. of | energy |   bns    |  score |Feature Points\r\nnumber|       |points|gyration|per vol.|buriedness|v*b^1.5 | D | A | Other\r\n------+-------+------+--------+--------+----------+--------+---+---+------\r\n   1   -112.83   212     4.40    -0.53     0.895    38.64    5   5    9\r\n   2    -67.80   168     4.10    -0.40     0.793    25.78    4   3    9\r\n   3    -45.24   129     3.37    -0.35     0.767    22.53    2   2    8\r\n   4    -44.37   106     3.18    -0.42     0.815    22.14    4   3    6\r\nAutoSite identified and characterized 4 clusters in 1.75 seconds, i.e. 0 hours 00 minutes 01.747343 seconds<\/pre>\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-d48a33c77bafc5f0084\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-outputfiles\" href=\"#tab-d48a33c77bafc5f0084\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-lightbulb fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Output files<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-outputfiles\" id=\"tab-d48a33c77bafc5f0084\">\n<p>The output files are created in the folder where the AutoSite program is being run.<\/p>\n<p>The previous command generated a log files containing the output printed to the terminal (1STP_AutoSiteSummary.log).<\/p>\n<p>I addition a folder called 1STP has been created. It contains:<\/p>\n<ul>\n<li>a set of files for cluster points (1 per cluster) in PDB format (1STP._CL.xxx.pdb)<\/li>\n<li>a set of files for feature points (1 per cluster) in PDB fomat (1STP_fp_xxx.pdb)<\/li>\n<li>a CSV file with values of the cluster scoring function for each cluster 91STP_summary.csv)<\/li>\n<li>the input file used to calculate grids with AutoGrid (rigidReceptor.gpf)<\/li>\n<li>the output files from the AutoGrid calculations (rigidReceptor.glg, rigidReceptor.x.map)<\/li>\n<\/ul>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":13,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-273","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/pages\/273","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/comments?post=273"}],"version-history":[{"count":16,"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/pages\/273\/revisions"}],"predecessor-version":[{"id":286,"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/pages\/273\/revisions\/286"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/autosite\/wp-json\/wp\/v2\/media?parent=273"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}