Team:UST Beijing/Modeling

From 2014.igem.org

(Difference between revisions)
(Prototype team page)
 
(19 intermediate revisions not shown)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
+
<html lang="en">
 +
  <head>
 +
    <meta charset="utf-8">
 +
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1">
 +
    <meta name="description" content="">
 +
    <meta name="author" content="">
 +
    <title>USTB iGEM14 Modeling</title>
-
{{CSS/Main}}
 
-
<html>
+
    <!-- Bootstrap core CSS -->
-
<!--main content -->
+
    <link href="https://2014.igem.org/Team:UST_Beijing/bootstrap/bootstrap.css?action=raw&ctype=text/css" rel="stylesheet">
-
<table width="70%" align="center">
+
    <link href="https://2014.igem.org/Team:UST_Beijing/bootstrap/docs.css?action=raw&ctype=text/css" rel="stylesheet">
 +
    <link href="https://2014.igem.org/Team:UST_Beijing/bootstrap/ihover.css?action=raw&ctype=text/css" rel="stylesheet">
-
<!--welcome box -->
+
    <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
-
<tr>
+
    <!--[if lt IE 9]>
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
      <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
    <![endif]-->
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
-
<br>
+
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:UST_Beijing/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
+
-
</td>
+
-
</tr>
+
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
    <!-- Custom styles for this template -->
-
<!-- end welcome box -->
+
-
<tr>  
+
-
<!--navigation menu -->
+
    <style>
-
<td align="center" colspan="3">
+
-
<table  width="100%">
+
    #footerlogo {
-
<tr heigth="15px"></tr>
+
      width: 250px;
-
<tr heigth="75px">
+
      height: 100px;
 +
    }
 +
    #modelform {
 +
      width: 900px;
 +
    }
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
      /* Removes the mysterious margin of footer */
-
<a href="https://2014.igem.org/Team:UST_Beijing"style="color:#000000">Home </a> </td>
+
    .bs-docs-footer {
 +
      margin-top: 0 !important;
 +
      border-top: 0 !important;
 +
    }
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      /* Removes default elements */
-
<a href="https://2014.igem.org/Team:UST_Beijing/Team"style="color:#000000"> Team </a> </td>
+
    #contentSub, #footer-box, #sitesub, #catlinks, #search-controls, #p-logo, .printfooter, .firstHeading, .visualClear {
 +
        display:none;
 +
      }
-
<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      #top-section {
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=UST_Beijing"style="color:#000000"> Official Team Profile </a></td>
+
        border: none;
 +
        height: 0px;
 +
        margin: 0px;
 +
      }
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
      #content {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Project"style="color:#000000"> Project</a></td>
+
        border: none;
 +
        background: transparent;
 +
        width: 100%;
 +
        padding: 0px;
 +
      }
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      p {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Parts"style="color:#000000"> Parts</a></td>
+
        margin: 0px;
 +
        padding: 0px;
 +
      }
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      body {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Modeling"style="color:#000000"> Modeling</a></td>
+
        margin: 0 0 0 0;
 +
        padding: 0;
 +
      }
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
      html, body {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Notebook"style="color:#000000"> Notebook</a></td>
+
        width: auto !important;
 +
        overflow-x: hidden !important;
 +
        height: 100% !important;
 +
        -webkit-overflow-scrolling: touch;
 +
      }
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      #top-section {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Safety"style=" color:#000000"> Safety </a></td>
+
        width: 1140px;
 +
        height: 0;
 +
        margin: 0 auto;
 +
        padding: 0;
 +
        border: none;
 +
      }
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
      #menubar {
-
<a href="https://2014.igem.org/Team:UST_Beijing/Attributions"style="color:#000000"> Attributions </a></td>
+
        font-size: 80%;
 +
        top: 0px;
 +
        margin: 0px;
 +
      /* Resizes the menubar to fix the links (default is 400px) */
 +
        width: auto;
 +
      }
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
+
      .left-menu:hover {
-
</tr>
+
        background-color: transparent;
-
</table>
+
      }
-
</tr>
+
-
</tr>
+
-
</td>
+
 +
      #menubar li a {
 +
      background: transparent;
 +
      color: transparent;
 +
    }
-
<tr> <td colspan="3"  height="15px"> </td></tr>
+
      #menubar:hover li a {
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
+
        background-color: rgba(255, 255, 255, 0.8);
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
        color: grey;
 +
      }
 +
      /* Removes "teams" from the menubar */
-
<!--modeling content -->
+
      #menubar > ul > li:last-child {
-
<tr><td colspan="3"> <h3>Modeling</h3></td></tr>
+
        display: none;}
-
</tr>
+
-
<tr>
+
      /* Customize the navbar */
-
<td width="45%"  valign="top">
+
-
<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
+
-
</td>
+
-
<td></td>
+
      /* Special class on .container surrounding .navbar, used for positioning it into place. */
-
<td></td>
+
      .navbar-wrapper {
-
</tr>
+
        position: absolute;
 +
        top: 0;
 +
        right: 0;
 +
        left: 0;
 +
        z-index: 20;
 +
      }
 +
      /* Flip around the padding for proper display in narrow viewports */
 +
      .navbar-wrapper > .container {
 +
        padding-right: 0;
 +
        padding-left: 0;
 +
      }
 +
      .navbar-wrapper .navbar {
 +
        padding-right: 15px;
 +
        padding-left: 15px;
 +
      }
 +
      .navbar-wrapper .navbar .container {
 +
        width: auto;
 +
      }
-
</table>
+
 
 +
      /* Customize the carousal */
 +
 
 +
      /* Carousel base class */
 +
 
 +
      .fill {
 +
          width: 100%;
 +
          height: 100%;
 +
          background-position: center;
 +
          -webkit-background-size: cover;
 +
          -moz-background-size: cover;
 +
          background-size: cover;
 +
          -o-background-size: cover;
 +
      }
 +
 
 +
      .carousel {
 +
        height: 480px;
 +
        margin-bottom: 60px;
 +
      }
 +
      /* Since positioning the image, we need to help out the caption */
 +
      .carousel-caption {
 +
        z-index: 10;
 +
      }
 +
 
 +
      /* Declare heights because of positioning of img element */
 +
      .carousel .item {
 +
        height: 480px;
 +
        background-color: #777;
 +
      }
 +
      .carousel-inner > .item > img {
 +
        position: absolute;
 +
        top: 0;
 +
        left: 0;
 +
        min-width: 100%;
 +
        height: 480px;
 +
      }
 +
 
 +
 
 +
 
 +
      /* Content */
 +
 
 +
      /* Center align the text within the three columns below the carousel */
 +
      .marketing .col-lg-4 {
 +
        margin-bottom: 20px;
 +
        text-align: center;
 +
      }
 +
      .marketing h2 {
 +
        font-weight: normal;
 +
      }
 +
      .marketing .col-lg-4 p {
 +
        margin-right: 10px;
 +
        margin-left: 10px;
 +
      }
 +
 
 +
 
 +
      /* Featurettes */
 +
 
 +
      .featurette-divider {
 +
        margin: 80px 0; /* Space out the Bootstrap <hr> more */
 +
      }
 +
 
 +
      /* Thin out the marketing headings */
 +
      .featurette-heading {
 +
        font-weight: 300;
 +
        line-height: 1;
 +
        letter-spacing: -1px;
 +
      }
 +
 
 +
 
 +
 
 +
      /* Responsive CSS */
 +
 
 +
      @media (min-width: 768px) {
 +
 
 +
        /* Navbar positioning foo */
 +
        .navbar-wrapper {
 +
          margin-top: 20px;
 +
        }
 +
        .navbar-wrapper .container {
 +
          padding-right: 15px;
 +
          padding-left: 15px;
 +
        }
 +
        .navbar-wrapper .navbar {
 +
          padding-right: 0;
 +
          padding-left: 0;
 +
        }
 +
 
 +
        /* The navbar becomes detached from the top, so we round the corners */
 +
        .navbar-wrapper .navbar {
 +
          border-radius: 4px;
 +
        }
 +
 
 +
        /* Bump up size of carousel content */
 +
        .carousel-caption p {
 +
          margin-bottom: 20px;
 +
          font-size: 21px;
 +
          line-height: 1.4;
 +
        }
 +
 
 +
        .featurette-heading {
 +
          font-size: 50px;
 +
        }
 +
      }
 +
 
 +
      @media (min-width: 992px) {
 +
        .featurette-heading {
 +
          margin-top: 120px;
 +
        }
 +
      }
 +
 
 +
    </style>
 +
 
 +
  </head>
 +
 
 +
<!-- navbar -->
 +
 
 +
  <body>
 +
    <div class="navbar-wrapper">
 +
      <div class="container">
 +
 
 +
        <div class="navbar navbar-inverse navbar-static-top" role="navigation">
 +
          <div class="container">
 +
            <div class="navbar-header">
 +
              <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
 +
                <span class="sr-only">Toggle navigation</span>
 +
                <span class="icon-bar"></span>
 +
                <span class="icon-bar"></span>
 +
                <span class="icon-bar"></span>
 +
              </button>
 +
              <a class="navbar-brand" href="https://2014.igem.org/Team:UST_Beijing">USTB iGEM14</a>
 +
            </div>
 +
            <div class="navbar-collapse collapse">
 +
              <ul class="nav navbar-nav">
 +
                <li><a href="https://2014.igem.org/Team:UST_Beijing">Home</a></li>
 +
                <li><a href="https://2014.igem.org/Team:UST_Beijing/Team">Team</a></li>
 +
                <li><a href="https://2014.igem.org/Team:UST_Beijing/Project">Project</a></li>
 +
                <li><a href="https://2014.igem.org/Team:UST_Beijing/Parts">Parts</a></li>
 +
                <li class="active" ><a href="https://2014.igem.org/Team:UST_Beijing/Modeling">Modeling</a></li>
 +
                <li><a href="https://2014.igem.org/Team:UST_Beijing/Outreach">Outreach</a></li>
 +
 
 +
 
 +
                <li class="dropdown">
 +
                  <a href="#notebook" class="dropdown-toggle" data-toggle="dropdown">Notebook <span class="caret"></span></a>
 +
                  <ul class="dropdown-menu" role="menu">
 +
                      <li><a href="https://2014.igem.org/Team:UST_Beijing/Footsteps">Footsteps</a></li>
 +
                      <li><a href="https://2014.igem.org/Team:UST_Beijing/Safety">Safety</a></li>
 +
                      <li><a href="https://2014.igem.org/Team:UST_Beijing/Attributions">Attributions</a></li>
 +
                  </ul>
 +
                </li>
 +
              </ul>
 +
            </div>
 +
          </div>
 +
        </div>
 +
 
 +
      </div>
 +
    </div>
 +
 
 +
 
 +
<!-- Carousel
 +
    <div id="myCarousel" class="carousel slide" data-ride="carousel">
 +
      <div class="carousel-inner">
 +
        <div class="item active" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Home_back2.jpg) no-repeat center center; background-size: cover;"></div>
 +
    </div>-->
 +
 
 +
<!-- Outreach Slideshow -->
 +
 
 +
    <div class="bs-docs-featurette">
 +
      <div class="container">
 +
        <h2 class="bs-docs-featurette-title">See the magic.</h2>
 +
        <p class="lead">Synthetic GLO gene was translated into protein, then the primary structure of which was uploaded onto SWISS-Model website for 3D structure construction.</p>
 +
 
 +
    <hr class="half-rule">
 +
 
 +
<!-- Full Page Image Background Carousel Header -->
 +
<div class="container" style="width:800px; height:480px; margin-bottom:60px">
 +
<div id="myCarousel" class="carousel slide">
 +
 
 +
    <!-- Wrapper for Slides -->
 +
    <div class="carousel-inner">
 +
        <div class="item active">
 +
            <!-- Set the first background image using inline CSS below. -->
 +
            <div class="fill" style="background-image:url('https://static.igem.org/mediawiki/2014/0/07/Model1.jpg');"></div>
 +
            <div class="carousel-caption">
 +
                <p></p>
 +
            </div>
 +
        </div>
 +
 
 +
    </div>
 +
 
 +
  </div>
 +
</div>
 +
 
 +
<hr class="half-rule">
 +
<p align="left" id="sticksCarouselMessage">Next the constructed 3D model was loaded into Chimera 8.1 and prepared. FAD was docked into model using auto dock vina; next pre-vitamin C, vitamin C and xylitol was individually docked into the catalytic site with FAD in situ. The table below shows the relative binding affinity of each putative substrate. The 3D model was calculated according to xylitol oxidase crystal structure (PDB code 2vfs). The result suggests that the 3D model was nearly accurate enough to distringuish putative substrates.</p>
 +
 
 +
  <hr class="half-rule">
 +
  <img id="modelform" align="center" src="https://static.igem.org/mediawiki/2014/d/d7/Modelform.JPG"></img>
 +
 
 +
 
 +
 
 +
</div>
 +
</div>
 +
 
 +
<!--    <div style="width:100%; height:45px; border:0; background-color: #ffffff;"></div> -->
 +
 
 +
 
 +
<!-- Footer  -->
 +
 
 +
<footer class="bs-docs-footer" role="contentinfo">
 +
  <div class="container">
 +
 
 +
  <div align="center"><img id="footerlogo" src="https://static.igem.org/mediawiki/2014/7/74/Headerlogo.png" alt="" class="img-responsive"></div>
 +
 
 +
  <p><br></p>
 +
 
 +
  <p><font size=2.5>Built with love<br>By the iGEM14 team of <a href="http://www.ustb.edu.cn/">University of Science and Technology Beijing</a></font></p>
 +
    </font>
 +
    </ul>
 +
  </div>
 +
</footer>
 +
 
 +
 
 +
 
 +
<!-- Bootstrap core JavaScript -->
 +
 
 +
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
 +
<script src="https://2014.igem.org/Team:UST_Beijing/bootstrap/bootstrap.js?action=raw"></script>
 +
<script src="https://2014.igem.org/Team:UST_Beijing/bootstrap/docs.js?action=raw"></script>
 +
 
 +
</body>
</html>
</html>

Latest revision as of 02:20, 17 October 2014

USTB iGEM14 Modeling

See the magic.

Synthetic GLO gene was translated into protein, then the primary structure of which was uploaded onto SWISS-Model website for 3D structure construction.

Next the constructed 3D model was loaded into Chimera 8.1 and prepared. FAD was docked into model using auto dock vina; next pre-vitamin C, vitamin C and xylitol was individually docked into the catalytic site with FAD in situ. The table below shows the relative binding affinity of each putative substrate. The 3D model was calculated according to xylitol oxidase crystal structure (PDB code 2vfs). The result suggests that the 3D model was nearly accurate enough to distringuish putative substrates.

Retrieved from "http://2014.igem.org/Team:UST_Beijing/Modeling"