{"version":"1.0","provider_name":"Biomedical Data Science Laboratory","provider_url":"https:\/\/bdsl.jbnu.ac.kr\/blog","author_name":"sphong","author_url":"https:\/\/bdsl.jbnu.ac.kr\/blog\/author\/sphong\/","title":"Prepare docking simulation for AutoDock Vina - Biomedical Data Science Laboratory","type":"rich","width":600,"height":338,"html":"<blockquote class=\"wp-embedded-content\" data-secret=\"Emwb6mKIFa\"><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/prepare-docking-simulation-for-autodock-vina\/\">Prepare docking simulation for AutoDock Vina<\/a><\/blockquote><iframe sandbox=\"allow-scripts\" security=\"restricted\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/prepare-docking-simulation-for-autodock-vina\/embed\/#?secret=Emwb6mKIFa\" width=\"600\" height=\"338\" title=\"&#8220;Prepare docking simulation for AutoDock Vina&#8221; &#8212; Biomedical Data Science Laboratory\" data-secret=\"Emwb6mKIFa\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\" class=\"wp-embedded-content\"><\/iframe><script>\n\/*! This file is auto-generated *\/\n!function(d,l){\"use strict\";l.querySelector&&d.addEventListener&&\"undefined\"!=typeof URL&&(d.wp=d.wp||{},d.wp.receiveEmbedMessage||(d.wp.receiveEmbedMessage=function(e){var t=e.data;if((t||t.secret||t.message||t.value)&&!\/[^a-zA-Z0-9]\/.test(t.secret)){for(var s,r,n,a=l.querySelectorAll('iframe[data-secret=\"'+t.secret+'\"]'),o=l.querySelectorAll('blockquote[data-secret=\"'+t.secret+'\"]'),c=new RegExp(\"^https?:$\",\"i\"),i=0;i<o.length;i++)o[i].style.display=\"none\";for(i=0;i<a.length;i++)s=a[i],e.source===s.contentWindow&&(s.removeAttribute(\"style\"),\"height\"===t.message?(1e3<(r=parseInt(t.value,10))?r=1e3:~~r<200&&(r=200),s.height=r):\"link\"===t.message&&(r=new URL(s.getAttribute(\"src\")),n=new URL(t.value),c.test(n.protocol))&&n.host===r.host&&l.activeElement===s&&(d.top.location.href=t.value))}},d.addEventListener(\"message\",d.wp.receiveEmbedMessage,!1),l.addEventListener(\"DOMContentLoaded\",function(){for(var e,t,s=l.querySelectorAll(\"iframe.wp-embedded-content\"),r=0;r<s.length;r++)(t=(e=s[r]).getAttribute(\"data-secret\"))||(t=Math.random().toString(36).substring(2,12),e.src+=\"#?secret=\"+t,e.setAttribute(\"data-secret\",t)),e.contentWindow.postMessage({message:\"ready\",secret:t},\"*\")},!1)))}(window,document);\n\/\/# sourceURL=https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-includes\/js\/wp-embed.min.js\n<\/script>\n","description":"Introduction Before performing molecular docking with AutoDock Vina, both the receptor (protein) and ligand (small molecule) structures must be properly prepared. This preparation includes assigning partial atomic charges, adding hydrogen atoms, and defining the flexible bonds of the ligand. AutoDock Vina uses the PDBQT format, which contains atomic coordinates, atom types, partial charges, and information [&hellip;]"}