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<html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1"><meta><title>NOTES and REFS</title><link rel="manifest" href="/manifest.json"><meta name="application-name" content="NOTES and REFS"><meta name="msapplication-TileImage" content="/img/avatar.png"><meta name="apple-mobile-web-app-capable" content="yes"><meta name="apple-mobile-web-app-title" content="NOTES and REFS"><meta name="apple-mobile-web-app-status-bar-style" content="default"><meta property="og:type" content="blog"><meta property="og:title" content="NOTES and REFS"><meta property="og:url" content="http://yoursite.com/"><meta property="og:site_name" content="NOTES and REFS"><meta property="og:locale" content="en_US"><meta property="og:image" content="http://yoursite.com/img/og_image.png"><meta property="article:author" content="shaoqz"><meta property="twitter:card" content="summary"><meta property="twitter:image" content="/img/og_image.png"><script type="application/ld+json">{"@context":"https://schema.org","@type":"BlogPosting","mainEntityOfPage":{"@type":"WebPage","@id":"http://yoursite.com"},"headline":"NOTES and REFS","image":["http://yoursite.com/img/og_image.png"],"author":{"@type":"Person","name":"shaoqz"},"description":""}</script><link rel="icon" href="/img/avatar.png"><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/all.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/styles/atom-one-light.css"><link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Ubuntu:wght@400;600&family=Source+Code+Pro"><link rel="stylesheet" href="/css/default.css"><style>body>.footer,body>.navbar,body>.section{opacity:0}</style><!--!--><!--!--><!--!--><!--!--><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/build/cookieconsent.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/lightgallery.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/justifiedGallery.min.css"><!--!--><!--!--><!--!--><script src="https://cdn.jsdelivr.net/npm/[email protected]/pace.min.js"></script><!--!--><!--!--><meta name="generator" content="Hexo 5.0.2"></head><body class="is-3-column"><nav class="navbar navbar-main"><div class="container"><div class="navbar-brand justify-content-center"><a class="navbar-item navbar-logo" href="/">SHAOQZ.CN</a></div><div class="navbar-menu"><div class="navbar-start"><a class="navbar-item is-active" href="/">Home</a><a class="navbar-item" href="/archives">Archives</a><a class="navbar-item" href="/categories">Categories</a><a class="navbar-item" href="/tags">Tags</a><a class="navbar-item" href="/ref-rank">Paper Ranking</a></div><div class="navbar-end"><a class="navbar-item" target="_blank" rel="noopener" title="GitHub" href="https://github.com/shaoqx"><i class="fab fa-github"></i></a><a class="navbar-item search" title="Search" href="javascript:;"><i class="fas fa-search"></i></a></div></div></div></nav><section class="section"><div class="container"><div class="columns"><div class="column order-2 column-main is-8-tablet is-8-desktop is-6-widescreen"><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-06-30T00:05:04.000Z" title="2023-06-30T00:05:04.000Z">2023-06-29</time></span><span class="level-item">Updated <time dateTime="2023-06-30T00:08:30.000Z" title="2023-06-30T00:08:30.000Z">2023-06-29</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Experiment/">Experiment</a></span><span class="level-item">a minute read (About 153 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/06/29/Exp-Culture-Medium-Preparation/">[Exp]Culture Medium Preparation</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/06/29/Exp-Culture-Medium-Preparation/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-06-28T20:49:32.000Z" title="2023-06-28T20:49:32.000Z">2023-06-28</time></span><span class="level-item">Updated <time dateTime="2023-07-12T21:37:34.514Z" title="2023-07-12T21:37:34.514Z">2023-07-12</time></span><span class="level-item"><a class="link-muted" href="/categories/Refs/">Refs</a><span> / </span><a class="link-muted" href="/categories/Refs/Enzyme/">Enzyme</a></span><span class="level-item">3 minutes read (About 464 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/06/28/RefNote-The-evolution-of-multiple-active-site-configurations-in-a-designed-enzyme/">RefNote: The evolution of multiple active site configurations in a designed enzyme KE07 & Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series</a></h1><div class="content"><blockquote>
<p>Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series<br><a target="_blank" rel="noopener" href="https://www.sciencedirect.com/science/article/pii/S0022283609015381?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0022283609015381?via%3Dihub</a></p>
</blockquote>
<blockquote>
<p>The evolution of multiple active site configurations in a designed enzyme<br><a target="_blank" rel="noopener" href="https://www.nature.com/articles/s41467-018-06305-y">https://www.nature.com/articles/s41467-018-06305-y</a></p>
</blockquote>
<ul>
<li>Important experimental protocol reference (background reaction; Arrhenius kinetics)</div><a class="article-more button is-small is-size-7" href="/2023/06/28/RefNote-The-evolution-of-multiple-active-site-configurations-in-a-designed-enzyme/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-05-24T22:48:25.000Z" title="2023-05-24T22:48:25.000Z">2023-05-24</time></span><span class="level-item">Updated <time dateTime="2023-05-25T00:02:47.000Z" title="2023-05-25T00:02:47.000Z">2023-05-24</time></span><span class="level-item"><a class="link-muted" href="/categories/Refs/">Refs</a><span> / </span><a class="link-muted" href="/categories/Refs/Enzyme/">Enzyme</a></span><span class="level-item">2 minutes read (About 352 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/05/24/RefNote-Electric-Field-Design%E5%90%88%E9%9B%86/">RefNote-Electric-Field-Design合集</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/05/24/RefNote-Electric-Field-Design%E5%90%88%E9%9B%86/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-05-08T21:02:28.000Z" title="2023-05-08T21:02:28.000Z">2023-05-08</time></span><span class="level-item">Updated <time dateTime="2023-05-08T22:24:18.837Z" title="2023-05-08T22:24:18.837Z">2023-05-08</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Tools/">Tools</a></span><span class="level-item">a few seconds read (About 104 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/05/08/HMMER-Notes/">HMMER Notes</a></h1><div class="content"><p>HMMer notes, avoid redundant searching</p></div><a class="article-more button is-small is-size-7" href="/2023/05/08/HMMER-Notes/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-04-15T03:18:36.000Z" title="2023-04-15T03:18:36.000Z">2023-04-14</time></span><span class="level-item">Updated <time dateTime="2023-04-15T03:19:54.415Z" title="2023-04-15T03:19:54.415Z">2023-04-14</time></span><span class="level-item"><a class="link-muted" href="/categories/Refs/">Refs</a><span> / </span><a class="link-muted" href="/categories/Refs/Enzyme/">Enzyme</a></span><span class="level-item">a few seconds read (About 109 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/04/14/RefNote-AsiteDesign/">RefNote: AsiteDesign</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/04/14/RefNote-AsiteDesign/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-04-15T02:56:52.000Z" title="2023-04-15T02:56:52.000Z">2023-04-14</time></span><span class="level-item">Updated <time dateTime="2023-04-15T03:00:03.813Z" title="2023-04-15T03:00:03.813Z">2023-04-14</time></span><span class="level-item"><a class="link-muted" href="/categories/Refs/">Refs</a><span> / </span><a class="link-muted" href="/categories/Refs/Enzyme/">Enzyme</a></span><span class="level-item">2 minutes read (About 325 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/04/14/RefNote-Using-High-Throughput-Molecular-Dynamics-Simulation-to-Enhance-the-Computational-Design-of-Kemp-Elimination-Enzymes/">RefNote: Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/04/14/RefNote-Using-High-Throughput-Molecular-Dynamics-Simulation-to-Enhance-the-Computational-Design-of-Kemp-Elimination-Enzymes/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-03-09T23:51:55.000Z" title="2023-03-09T23:51:55.000Z">2023-03-09</time></span><span class="level-item">Updated <time dateTime="2023-09-01T23:49:29.004Z" title="2023-09-01T23:49:29.004Z">2023-09-01</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Experiment/">Experiment</a></span><span class="level-item">a minute read (About 120 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/03/09/Exp-Kinetic-Assay-KE/">[Exp] Kinetic Assay KE</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/03/09/Exp-Kinetic-Assay-KE/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-02-01T20:45:53.000Z" title="2023-02-01T20:45:53.000Z">2023-02-01</time></span><span class="level-item">Updated <time dateTime="2023-04-15T02:54:34.463Z" title="2023-04-15T02:54:34.463Z">2023-04-14</time></span><span class="level-item"><a class="link-muted" href="/categories/Refs/">Refs</a><span> / </span><a class="link-muted" href="/categories/Refs/code-O/">code-O</a></span><span class="level-item">a few seconds read (About 30 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/02/01/RefNote-code-O/">RefNote: mechanisms of oxygen resistance of enzyme</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/02/01/RefNote-code-O/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2023-01-19T22:41:51.000Z" title="2023-01-19T22:41:51.000Z">2023-01-19</time></span><span class="level-item">Updated <time dateTime="2023-06-30T00:03:49.000Z" title="2023-06-30T00:03:49.000Z">2023-06-29</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Experiment/">Experiment</a></span><span class="level-item">3 minutes read (About 444 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2023/01/19/Exp-Sterilization/">[Exp]Sterilization</a></h1><div class="content">This article is locked. This might include some personal or unpublished info.</div><a class="article-more button is-small is-size-7" href="/2023/01/19/Exp-Sterilization/#more">Read more</a></article></div><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted <time dateTime="2022-12-22T02:06:42.000Z" title="2022-12-22T02:06:42.000Z">2022-12-21</time></span><span class="level-item">Updated <time dateTime="2022-12-22T03:32:18.936Z" title="2022-12-22T03:32:18.936Z">2022-12-21</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a></span><span class="level-item">a minute read (About 174 words)</span></div></div><h1 class="title is-3 is-size-4-mobile"><a class="link-muted" href="/2022/12/21/Enzyme-s-Toolbox-for-Catalysis/">Enzyme's Toolbox for Catalysis</a></h1><div class="content">This article is locked. 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