The journey of a cheminformatics scientist
Drug discovery is a complex and resource-intensive process that involves synthesizing new compounds, often using well-established chemical reactions. While these methods have proven effective, there can be certain biases in the types of molecular structures they produce. For example, common reactions such as Suzuki or amide coupling tend to favor specific molecular frameworks, potentially limiting…
Introduction I want to introduce you to ChemX, a Python-based program I developed during a hackathon in 2019. You can use it to build virtual chemical libraries using fragment analogues to the building blocks of the target molecule. Using the RDKit library, ChemX assembles chemically similar fragments to create a virtual chemical library. What ChemX…
In this tutorial, I will show how to generate bar chats with chemical structures using python and rdkit. I am adopting the code from Andres Berejnoi’s code repository. His code works with any image as long as you can represent the image as numpy array. For the code, you will need the following python libraries: pandas,…
In this tutorial, I will show how to generate reaction-based molecules with python code tutorials. I previously developed PKS Enumerator and SIME software tools which are used to design virtual libraries of macrocycles/macrolides. Both were based on a string- or template-based enumeration, and I will write a tutorial on how to do that in a…
Please check out the previous blog posts from this series if you haven’t done so already: Part 1 algorithm for k-fold Cross-Validation Part 2A of the Nested Cross-Validation & Cross-Validation Series where I went through a python tutorial on implementing k-fold CV regressors using random forest (RF) from scikit-learn with a simple cheminformatics dataset with descriptors…
This is the last of the five-part series tutorial of the blog post, Computing Molecular Descriptors – Intro, in the context of drug discovery. The goal of this post to explain the python code on creating new descriptors such as MRC (developed in MacrolactoneDB study) and using Mordred descriptors. What are MRC descriptors? MRC descriptors were…