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Navan Chauhan <br> <a href="/feed.rss">RSS</a></p></div> - </div> -</div> - -<script> -let phrases = [ - "Something Funny", "Veni, vidi, vici", "Alea iacta est", "In vino veritas", "Acta, non verba", "Castigat ridendo mores", - "Cui bono?", "Memento vivere", "अहम् ब्रह्मास्मि", "अनुगच्छतु प्रवाहं", "चरन्मार्गान्विजानाति", "coq de cheval", "我愛啤酒" - ]; - -let new_phrase = phrases[Math.floor(Math.random()*phrases.length)]; - -let lead = document.getElementById("random-lead"); -lead.innerText = new_phrase; -</script> - <div class="content container"> - - <div class="post"> - <h1 id="cheminformatics-on-the-web-2021">Cheminformatics on the Web (2021)</h1> - -<p>Here, I have compiled a list of some libraries and possible ideas. -I, personally, like static websites which don't require a server side application and can be hosted on platforms like GitHub Pages. -Or, just by opening the HTML file and running it in your browser. -WebAssembly (Wasm) has made running code written for other platforms on the web relatively easier. -Combine Wasm with some pure JavaScript libraries, and you get a platform to quickly amp up your speed in some common tasks.</p> - -<h2 id="rdkit">RDKit</h2> - -<p>RDKit bundles a minimal JavaScript Wrapper in their core RDKit suite. -This is perfect for generating 2D Figures (HTML5 Canva/SVGs), Canonical SMILES, Descriptors e.t.c</p> - -<h3 id="substructure-matching">Substructure Matching</h3> - -<p>This can be used to flag undesirable functional groups in a given compound. -Create a simple key:value pairs of name:SMARTS and use it to highlight substructure matches. -Thus, something like PostEra's Medicinal Chemistry Alert can be done with RDKit-JS alone.</p> - -<p><img src="/assets/posts/cheminformatics-web/postera-demo.png" alt="PostEra Demo" /></p> - -<h3 id="computing-properties">Computing Properties</h3> - -<p>This is useful to calculate basic properties of a given compound.</p> - -<p><img src="/assets/posts/cheminformatics-web/rdkit-demo.png" alt="RDKit-JS Demo" /></p> - -<h2 id="webina-molecular-docking">Webina - Molecular Docking</h2> - -<p>Webina is a JavaScript/Wasm library that runs AutoDock Vina, which can enable you to run Molecular Docking straight in the browser itself.</p> - -<p><img src="/assets/posts/cheminformatics-web/webina-demo.png" alt="Webina Demo" /></p> - -<p>Obviously, it takes a few hits in the time to complete the docking because the code is transpiled from C++ to Wasm. -But, the only major drawback (for now) is that it uses SharedArrayBuffer. -Due to Spectre, this feature was disabled on all browsers. -Currently, only Chromium-based and Firefox browsers have reimplemented and enabled it. -Hopefully, soon, this will be again supported by all major browsers.</p> - -<h2 id="machine-learning">Machine Learning</h2> - -<p>Frameworks have now evolved enough to allow exporting models to be able to run them through JavaScript/Wasm backend. -An example task can be <strong>NER</strong> or Named-entity Recognition. -It can be used to extract compounds or diseases from a large blob of text and then matched with external references. -Another example is target-prediction right in the browser: <a rel="noopener" target="_blank" href="http://chembl.blogspot.com/2021/03/target-predictions-in-browser-with.html">CHEMBL - Target Prediction in Browser</a></p> - -<p>CHEMBL Group is first training the model using PyTorch (A Python ML Library), then converting it to the ONNX runtime. -A model like this can be directly implemented in TensorFlow, and then exported to be able to run with TensorFlow.js</p> - -<h2 id="cheminfo-to-web">Cheminfo-to-web</h2> - -<p>The project aims to port cheminformatics libraries into JavaScript via Emscripten. -They have ported InChI, Indigo, OpenBabel, and OpenMD</p> - -<h3 id="kekulejs">Kekule.js</h3> - -<p>It is written by @partridgejiang, who is behind the Cheminfo-to-web project</p> - -<blockquote> - <p>It is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.</p> -</blockquote> - -<h2 id="browser-extensions">Browser Extensions</h2> - -<p>The previous machine learning examples can be packaged as browser-extensions to perform tasks on the article you are reading. -With iOS 15 bringing WebExtensions to iOS/iPadOS, the same browser extension source code can be now used on Desktop and Mobile Phones. -You can quickly create an extension to convert PDB codes into links to RCSB, highlight SMILES, highlight output of NER models, e.t.c</p> - -<h2 id="conclusion">Conclusion</h2> - -<p>I have not even touched all the bases of cheminformatics for the web here. -There is still a lot more to unpack. -Hopefully, this encourages you to explore the world of cheminformatics on the web.</p> - -<h2 id="further-reading">Further Reading</h2> - -<p><a rel="noopener" target="_blank" href="https://blueobelisk.github.io/greasemonkey.html">Blueobelisk Userscripts</a></p> - -<p><a rel="noopener" target="_blank" href="https://depth-first.com/articles/2019/05/01/javascript-for-cheminformatics-part-2/">JavaScript for Cheminformatics</a></p> - -<p><a rel="noopener" target="_blank" href="https://unpkg.com/@rdkit/rdkit@2021.3.3/Code/MinimalLib/dist/GettingStartedInJS.html">Getting Started with RDKit-JS</a></p> - - </div> - <blockquote>If you have scrolled this far, consider subscribing to my mailing list <a href="https://listmonk.navan.dev/subscription/form">here.</a> You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.</blockquote> - 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