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<section id="atom-modeling-pipeline-ampl-for-drug-discovery">
<h1>ATOM Modeling PipeLine (AMPL) for Drug Discovery<a class="headerlink" href="#atom-modeling-pipeline-ampl-for-drug-discovery" title="Permalink to this headline"></a></h1>
<p><strong>AMPL</strong> is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.</p>
<p>The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools. AMPL is an end-to-end data-driven modeling pipeline to generate machine learning models that can predict key safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters.</p>
<section id="features">
<h2>Features<a class="headerlink" href="#features" title="Permalink to this headline"></a></h2>
<p>AMPL enables tasks for modeling and prediction from data ingestion to data analysis and can be broken down into the following stages:</p>
<ul class="simple">
<li><p>Data ingestion and curation</p></li>
<li><p>Featurization</p></li>
<li><p>Model training and tuning</p></li>
<li><p>Prediction generation</p></li>
<li><p>Visualization and analysis</p></li>
<li><p>Details of running specific features are within the parameter (options) documentation.</p></li>
</ul>
<p>More detailed documentation is in the library documentation.</p>
</section>
<section id="built-with">
<h2>Built with<a class="headerlink" href="#built-with" title="Permalink to this headline"></a></h2>
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<li><p><a class="reference external" href="https://github.com/deepchem/deepchem">DeepChem</a>: The basis for the graph convolution models</p></li>
<li><p><a class="reference external" href="http://www.rdkit.org">RDKit</a>: Molecular informatics library</p></li>
<li><p><a class="reference external" href="https://github.com/mordred-descriptor/mordred">Mordred</a>: Chemical descriptors</p></li>
<li><p>Other Python package dependencies</p></li>
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<h2>User guide<a class="headerlink" href="#user-guide" title="Permalink to this headline"></a></h2>
<p>A step-by-step guide to getting started with MolVS.</p>
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<li class="toctree-l1"><a class="reference internal" href="guide/advanced_ampl_usage.html">Advanced AMPL Usage</a></li>
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<h2>Useful links<a class="headerlink" href="#useful-links" title="Permalink to this headline"></a></h2>
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<li><p><a class="reference external" href="https://github.com/ATOMScience-org/AMPL">ATOM Data-Driven Modeling Pipeline on GitHub</a></p></li>
<li><p><a class="reference external" href="https://github.com/ATOMScience-org/AMPL/blob/master/atomsci/ddm/docs/PARAMETERS.md">Pipeline parameters (options)</a></p></li>
<li><p><a class="reference external" href="https://ampl.readthedocs.io/en/latest/index.html">Library documentation</a></p></li>
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