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+---
+date: 2021-06-26 13:04
+description: Summarising Cheminformatics on the web in 2021.
+tags: Cheminformatics, JavaScript
+---
+
+# Cheminformatics on the Web (2021)
+
+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.
+
+## RDKit
+
+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
+
+### Substructure Matching
+
+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.
+
+![PostEra Demo](/assets/posts/cheminformatics-web/postera-demo.png)
+
+### Computing Properties
+
+This is useful to calculate basic properties of a given compound.
+
+![RDKit-JS Demo](/assets/posts/cheminformatics-web/rdkit-demo.png)
+
+## Webina - Molecular Docking
+
+Webina is a JavaScript/Wasm library that runs AutoDock Vina, which can enable you to run Molecular Docking straight in the browser itself.
+
+![Webina Demo](/assets/posts/cheminformatics-web/webina-demo.png)
+
+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.
+
+## Machine Learning
+
+Frameworks have now evolved enough to allow exporting models to be able to run them through JavaScript/Wasm backend.
+An example task can be **NER** 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: [CHEMBL - Target Prediction in Browser](http://chembl.blogspot.com/2021/03/target-predictions-in-browser-with.html)
+
+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
+
+## Cheminfo-to-web
+
+The project aims to port cheminformatics libraries into JavaScript via Emscripten.
+They have ported InChI, Indigo, OpenBabel, and OpenMD
+
+### Kekule.js
+
+It is written by @partridgejiang, who is behind the Cheminfo-to-web project
+
+> It is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
+
+## Browser Extensions
+
+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
+
+
+## Conclusion
+
+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.
+
+## Further Reading
+
+[Blueobelisk Userscripts](https://blueobelisk.github.io/greasemonkey.html)
+
+[JavaScript for Cheminformatics](https://depth-first.com/articles/2019/05/01/javascript-for-cheminformatics-part-2/)
+
+[Getting Started with RDKit-JS](https://unpkg.com/@rdkit/rdkit@2021.3.3/Code/MinimalLib/dist/GettingStartedInJS.html)