File size: 7,154 Bytes
8896a5f |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 |
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>D-SCRIPT: Deep Learning PPI Prediction — D-SCRIPT v1.0-beta documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Installation" href="installation.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="#" class="icon icon-home"> D-SCRIPT
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="data.html">Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="api/index.html">API</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="#">D-SCRIPT</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="#" class="icon icon-home"></a> »</li>
<li>D-SCRIPT: Deep Learning PPI Prediction</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="d-script-deep-learning-ppi-prediction">
<h1>D-SCRIPT: Deep Learning PPI Prediction<a class="headerlink" href="#d-script-deep-learning-ppi-prediction" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><p><a class="reference external" href="http://dscript.csail.mit.edu">D-SCRIPT Home Page</a></p></li>
<li><p><a class="reference external" href="usage.html#quick-start">Quick Start</a></p></li>
</ul>
<p>D-SCRIPT is a deep learning method for predicting a physical interaction between two proteins given just their sequences.
It generalizes well to new species and is robust to limitations in training data size.
Its design reflects the intuition that for two proteins to physically interact, a subset of amino acids from each protein should be in contact with the other.
The intermediate stages of D-SCRIPT directly implement this intuition, with the penultimate stage in D-SCRIPT being a rough estimate of the inter-protein
contact map of the protein dimer. This structurally-motivated design enhances the interpretability of the results and, since structure is more conserved
evolutionarily than sequence, improves generalizability across species.</p>
<p>If you use D-SCRIPT, please cite “Sequence-based prediction of protein-protein interactions: a structure-aware interpetable deep learning model”
by <a class="reference external" href="http://samsledje.github.io/">Sam Sledzieski</a>, <a class="reference external" href="http://people.csail.mit.edu/rsingh/">Rohit Singh</a>, <a class="reference external" href="http://www.cs.tufts.edu/~cowen/">Lenore Cowen</a>, and <a class="reference external" href="http://people.csail.mit.edu/bab/">Bonnie Berger</a> [link TBD].</p>
</div>
<div class="section" id="table-of-contents">
<h1>Table of contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="data.html">Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="api/index.html">API</a></li>
</ul>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
</ul>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="installation.html" class="btn btn-neutral float-right" title="Installation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2020, Samuel Sledzieski, Rohit Singh.
</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html> |