These are useful scripts I usually use in my research. Will try to update the list regularly.
Purpose: The script is used to standardize the structure into proper ones using the SMILES, then add a column of chemical representation in 2D format and IUPAD readout using a deep learning model. The script was gathered from different sources.
Script: Google Colab
Purpose: To evaluate the capability of a virtual screening method in enrichment actives among the pool of actives and inactives.
Script: Google Colab
Purpose: Automate the molecular docking process using AutoDock Vina. The script was written in Bash therefore natively compatible with Linux. For Windows, I recommend installing and setting up a path to cygwin64/bash.exe to implement the script.
Scripts: GitHub repository
Purpose: I wrote this notebook to automate the visual analysis of MD trajectories from the GROMACS program. The script assumes that you put it in the parent folder in which the subfolders are different protein-ligand complexes that have undergone MD simulation and have generated the necessary .xvg files for visualization.
Scripts: GitHub repository
