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. @@ -52,12 +52,12 @@ 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. @@ -65,13 +65,13 @@ Thus, something like PostEra's Medicinal Chemistry Alert can be done with RDKit-

PostEra Demo

Computing Properties

This is useful to calculate basic properties of a given compound.

RDKit-JS Demo

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.

@@ -83,7 +83,7 @@ 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. @@ -93,12 +93,12 @@ Another example is target-prediction right in the browser: 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

@@ -106,19 +106,19 @@ They have ported InChI, Indigo, OpenBabel, and OpenMD

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.

-- cgit v1.2.3 From 9e620084e57378952c1a7f8e0a772ebebd18932b Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 20:35:09 -0600 Subject: quick fix --- docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html') diff --git a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html index 1120ca0..2947c21 100644 --- a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html +++ b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html @@ -6,13 +6,13 @@ - id="cheminformatics-on-the-web-2021">Cheminformatics on the Web (2021) + Cheminformatics on the Web (2021) - Cheminformatics on the Web (2021)" /> - Cheminformatics on the Web (2021)" /> + + -- cgit v1.2.3 From 01ff93c9c16867216f2d249664803860e1d6d5eb Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 22:49:40 -0600 Subject: generate new theme --- ...2021-06-26-Cheminformatics-On-The-Web-2021.html | 55 +++++++++++++++------- 1 file changed, 37 insertions(+), 18 deletions(-) (limited to 'docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html') diff --git a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html index 2947c21..a249433 100644 --- a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html +++ b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html @@ -2,14 +2,26 @@ - + + + + + Cheminformatics on the Web (2021) + + + + + + + - Cheminformatics on the Web (2021) - @@ -29,21 +41,27 @@ - - - + + +

- +

Cheminformatics on the Web (2021)

Here, I have compiled a list of some libraries and possible ideas. @@ -126,14 +144,15 @@ Hopefully, this encourages you to explore the world of cheminformatics on the we

Getting Started with RDKit-JS

If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.

-- cgit v1.2.3 From de19543d7fb44d343b052dc9b34ede78620c4a46 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 23:36:55 -0600 Subject: Generate --- .../2021-06-26-Cheminformatics-On-The-Web-2021.html | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) (limited to 'docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html') diff --git a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html index a249433..a889cb1 100644 --- a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html +++ b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html @@ -46,7 +46,7 @@ + +

-- cgit v1.2.3 From a982ceab0b45609991179b3020a00260eed6f798 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 23:45:59 -0600 Subject: css --- docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html | 1 + 1 file changed, 1 insertion(+) (limited to 'docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html') diff --git a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html index a889cb1..68a4c25 100644 --- a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html +++ b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html @@ -5,6 +5,7 @@ + Cheminformatics on the Web (2021) -- cgit v1.2.3

Cheminformatics on the Web (2021)

Cheminformatics on the Web (2021)

RDKit

RDKit

Substructure Matching

Substructure Matching

Computing Properties

Computing Properties

Webina - Molecular Docking

Webina - Molecular Docking

Machine Learning

Machine Learning

Cheminfo-to-web

Cheminfo-to-web

Kekule.js

Kekule.js

Browser Extensions

Browser Extensions

Conclusion

Conclusion

Further Reading

Further Reading

Navan

Cheminformatics on the Web (2021)

Navan