Cheminformatics

Here are some demonstrations of applications of chemoinformatics tools for various problems using python. I use several free available modules for chemistry:RDKit, mordred. Most of the data in the notebooks was obtained from MoleculeNet.

Solubility prediction from the chemical structure. ML algorithm to predict solubility from molecular structure using RDKit and sklearn. See notebook.

Prediction of drug activity for androgen receptor. ML algorithm to predicit activity of molecule as drug for androgen receptor. Using QSAR descriptors (obtained by mordred). See notebook.

Chemical space of HIV drugs. Simple exploration of chemical space of HIV drugs. See notebook.

Searching for active fragments in HIV drugs. Simple ML algorithm to predict activity of the molecule and results interpreted using lime module. See notebook.

Molecular dynamics (MD)

Creation of coordinate file (GRO/PDB) from topology (RTP). See notebook.

Optimalization of bonded parameters*. Simple script to optimize bonded parameters for coarse-grained representation of a molecule. See notebook.

Simulations of self-assembly on graphite flake. This was part of my research and has been published (see article). See notebook.

Other