The journey of a cheminformatics scientist
This is part 2A of the Nested Cross-Validation & Cross-Validation Series. I will go through a python tutorial on implementing k-fold CV regressors using random forest (RF) from scikit-learn with the first dataset: (A) a simple cheminformatics dataset with descriptors and endpoints of interest. In Part 2B, I will cover the same python tutorial for…
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…
This is part-4 from 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 computing 2D RDKit descriptors and exporting them as CSV files. First, install the required library packages using miniconda. The code for RDKit_2D class that…
This is from the five-part series tutorial of the previous blog post, Computing Molecular Descriptors – Intro in the context of drug discovery. The goal of this post to explain the python code on computing MACCS fingerprints. Please read this blog to familiarize yourself with MACCS. The 166 public keys (fragment definitions) of MACCS in…
I will write a five-part series tutorial on implementing the python code to compute different sets of 2D molecular descriptors & fingerprints which are highly used in the context of drug discovery. Many thanks to the first-year Ph.D. students who request me to write tutorials on cheminformatics topics such as these. I welcome readers to…