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--- a +++ b/docs/build/html/notes/DTI.html @@ -0,0 +1,358 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>What is drug repurposing, virtual screening and drug-target interaction prediction? — DeepPurpose 0.0.1 documentation</title> + + + + + + + + + <script type="text/javascript" src="../_static/js/modernizr.min.js"></script> + + + <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 src="../_static/language_data.js"></script> + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <link 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Repurposing</a></li> +<li class="toctree-l2"><a class="reference internal" href="#virtual-screening">Virtual Screening</a></li> +<li class="toctree-l2"><a class="reference internal" href="#drug-target-interaction">Drug-Target Interaction</a></li> +</ul> +</li> +</ul> +<p class="caption"><span class="caption-text">How to run</span></p> +<ul> +<li class="toctree-l1"><a class="reference internal" href="download.html">Download Code & Install</a><ul> +<li class="toctree-l2"><a class="reference internal" href="download.html#download-code">Download Code</a></li> +<li class="toctree-l2"><a class="reference internal" href="download.html#first-time-usage-setup-conda-environment">First time usage: setup conda environment</a></li> +<li class="toctree-l2"><a class="reference internal" href="download.html#second-time-and-later">Second time and later</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="casestudy.html">Case Study</a></li> +</ul> +<p class="caption"><span class="caption-text">Package Reference</span></p> +<ul> +<li class="toctree-l1"><a class="reference internal" href="models.html">DeepPurpose.models</a><ul> +<li class="toctree-l2"><a class="reference internal" href="dtba/classifier.html">Classifier</a></li> +<li class="toctree-l2"><a class="reference internal" href="dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/transformer.html">Transformer</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/cnnrnn.html">CNN+RNN</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/cnn.html">CNN</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoders/mlp.html">MLP</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="dataset.html">DeepPurpose.dataset</a><ul> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_training_dataset_drug_target_pairs.html">read_file_training_dataset_drug_target_pairs</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_virtual_screening_drug_target_pairs.html">read_file_virtual_screening_drug_target_pairs</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_repurposing_library.html">load bioarray dataset (read_file_training_dataset_bioassay)</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/read_file_target_sequence.html">read_file_target_sequence</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/download_BindingDB.html">download_DrugTargetCommons</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/process_BindingDB.html">process_BindingDB</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_process_DAVIS.html">load_process_DAVIS</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_process_KIBA.html">load_process_KIBA</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_antiviral_drugs.html">load_antiviral_drugs</a></li> +<li class="toctree-l2"><a class="reference internal" href="data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="chemutils.html">DeepPurpose.chemutils</a><ul> +<li class="toctree-l2"><a class="reference internal" href="chem/onek_encoding_unk.html">DeepPurpose.chemutils.onek_encoding_unk</a></li> +<li class="toctree-l2"><a class="reference internal" href="chem/atom_features.html">DeepPurpose.chemutils.atom_features</a></li> +<li class="toctree-l2"><a class="reference internal" href="chem/bond_features.html">DeepPurpose.chemutils.bond_features</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="oneliner.html">DeepPurpose.oneliner</a><ul> +<li class="toctree-l2"><a class="reference internal" href="oneliner_folder/repurpose.html">DeepPurpose.oneliner.repurpose</a></li> +<li class="toctree-l2"><a class="reference internal" href="oneliner_folder/virtual_screening.html">DeepPurpose.oneliner.virtual_screening</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="model_helper.html">DeepPurpose.model_helper</a></li> +<li class="toctree-l1"><a class="reference internal" href="utils.html">DeepPurpose.utils</a></li> +</ul> +<p class="caption"><span class="caption-text">Importance Function</span></p> +<ul> +<li class="toctree-l1"><a class="reference internal" href="model.html">Drug Target Binding Affinity (DTBA) Model</a><ul> +<li class="toctree-l2"><a class="reference internal" href="dtba/classifier.html">Classifier</a></li> +<li class="toctree-l2"><a class="reference internal" href="dtba/dbta.html">Drug Target Binding Affinity (DTBA) Model</a></li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="encoder.html">Drug/Target Encoder</a><ul> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#drug-encoding">Drug encoding</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#target-encoding">Target encoding</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#encoder-model">Encoder Model</a></li> +<li class="toctree-l2"><a class="reference internal" href="encoder.html#technical-details">Technical Details</a><ul> +<li class="toctree-l3"><a class="reference internal" href="encoders/transformer.html">Transformer</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/cnnrnn.html">CNN+RNN</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/cnn.html">CNN</a></li> +<li class="toctree-l3"><a class="reference internal" href="encoders/mlp.html">MLP</a></li> +</ul> +</li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="process_data.html">Processing Data</a><ul> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#drug-target-binding-benchmark-dataset">Drug-Target Binding Benchmark Dataset</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#repurposing-dataset">Repurposing Dataset</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#bioassay-data-for-covid-19">Bioassay Data for COVID-19</a></li> +<li class="toctree-l2"><a class="reference internal" href="process_data.html#covid-19-targets">COVID-19 Targets</a><ul> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_training_dataset_bioassay.html">read_file_training_dataset_bioassay</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_training_dataset_drug_target_pairs.html">read_file_training_dataset_drug_target_pairs</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_virtual_screening_drug_target_pairs.html">read_file_virtual_screening_drug_target_pairs</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_repurposing_library.html">load bioarray dataset (read_file_training_dataset_bioassay)</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/read_file_target_sequence.html">read_file_target_sequence</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/download_BindingDB.html">download_DrugTargetCommons</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/process_BindingDB.html">process_BindingDB</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_process_DAVIS.html">load_process_DAVIS</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_process_KIBA.html">load_process_KIBA</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_AID1706_txt_file.html">load_AID1706_txt_file</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_AID1706_SARS_CoV_3CL.html">load_AID1706_SARS_CoV_3CL</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_antiviral_drugs.html">load_antiviral_drugs</a></li> +<li class="toctree-l3"><a class="reference internal" href="data/load_broad_repurposing_hub.html">load_broad_repurposing_hub</a></li> +</ul> +</li> +</ul> +</li> +<li class="toctree-l1"><a class="reference internal" href="configuration.html">Configuration</a></li> +<li class="toctree-l1"><a class="reference internal" href="utility_function.html">Utility Function</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="../index.html">DeepPurpose</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="../index.html">Docs</a> »</li> + + <li>What is drug repurposing, virtual screening and drug-target interaction prediction?</li> + + + <li class="wy-breadcrumbs-aside"> + + + <a href="../_sources/notes/DTI.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="what-is-drug-repurposing-virtual-screening-and-drug-target-interaction-prediction"> +<h1>What is drug repurposing, virtual screening and drug-target interaction prediction?<a class="headerlink" href="#what-is-drug-repurposing-virtual-screening-and-drug-target-interaction-prediction" title="Permalink to this headline">¶</a></h1> +<div class="section" id="drug-repurposing"> +<h2>Drug Repurposing<a class="headerlink" href="#drug-repurposing" title="Permalink to this headline">¶</a></h2> +<p>Drug repurposing aims to repivot an existing drug to a new therapy.</p> +</div> +<div class="section" id="virtual-screening"> +<h2>Virtual Screening<a class="headerlink" href="#virtual-screening" title="Permalink to this headline">¶</a></h2> +<dl class="simple"> +<dt>Virtual screening means to use computer software to automatically screen</dt><dd><p>a huge space of potential drug-target pairs to obtain a predicted binding score.</p> +</dd> +</dl> +</div> +<div class="section" id="drug-target-interaction"> +<h2>Drug-Target Interaction<a class="headerlink" href="#drug-target-interaction" title="Permalink to this headline">¶</a></h2> +<p>Both of these tasks are able to save cost, time, and facilitate drug discovery. +Deep learning has shown strong performance in repurposing and screening. +It relies on the accurate and fast prediction of a fundamental task: +drug-target interaction prediction. +DTI prediction task aims to predict the input drug target pair’s interaction probability or binding score. +Given a powerful DTI model that is able to generalize over a new unseen dataset, +we can then extend to repurposing/screening. +For repurposing, given a new target of interest, +we can first pair it to a repurposing drug library. +Then this list of input drug-target pairs is fed into the trained DTI model, +which will output the predicted binding score. +Similarly, for virtual screening, given a list of screening drug-target pairs we want, +the DTI model can output the predicted interaction binding scores. +We can then rank the predicted outcome based on their binding scores and +test the top-k options in the wet lab after manual inspection. +DeepPurpose automates this process. By only requiring one line of code, +it aggregates five pretrained deep learning models and retrieves a list of ranked potential outcomes.</p> +<p>Identifying Drug-Target Interactions (DTI) will greatly narrow down +the scope of search of candidate medications, +and thus can plays a pivotal role in drug discovery. +Drugs usually interact with one or more proteins to achieve their functions. +However, discovering novel interactions between drugs +and target proteins is crucial for the development of new drugs, +since the aberrant expression of proteins may cause side effects of drugs.</p> +<p>Considering that in vitro experiments are extremely costly and time-consuming, +high efficiency computational prediction methods could +serve as promising strategies for drug-target interaction (DTI) prediction. +In this project, our goal is to focus on deep learning approaches +for drug-target interaction (DTI) prediction.</p> +</div> +</div> + + + </div> + + </div> + <footer> + + <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> + + <a href="download.html" class="btn btn-neutral float-right" title="Download Code & Install" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a> + + + <a href="introduction.html" class="btn btn-neutral float-left" title="Features of DeepPurpose" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a> + + </div> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2020, Kexin Huang, Tianfan Fu + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/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> \ No newline at end of file