The Chemical Data Processing Toolkit

📐 Symmetry-corrected RMSD in Python

A curated list of awesome AI and Bioinformatics.

Source code and documentation of a computer assisted synthesis planning (CASP) tool used for the analysis of reaction datasets.

The repository for the course "Machine Learning in Drug Design" taught at the Jagiellonian University in 2023. The page is hosted by the machine learning research group GMUM.

LigTMap currently supports prediction for 17 protein target classes that include 6000+ protein targets.

The repository of the course "Machine Learning in Drug Design" at the Jagiellonian University, Kraków, Poland. The page is hosted by the machine learning research group GMUM.

Maximal Unbiased Benchmarking Datasets for Histone Deacetylases and Sirtuin Family

QSAR models and data used for MAO-A and MAO-B virtual screening.

Here I provide some code that enables users to calculate CNS MPO score for their molecules, based on the SMILES and known pKa values.

CSearch: Chemical Space Search via Virtual Synthesis and Global Optimization

MUBD-DecoyMaker2.0 is an easy-to-use computational tool to build maximal unbiased benchmarking sets for assessment of virtual screening approaches.

Energen is a pipeline for generating a dataset of protein-ligand complexes (Enerplex). It integrates absolute free energy perturbation (AFEP) and MM/XBSA energy calculations within a transformer-based latent space for advanced analysis.

An R script that calculates a similarity matrix for a list of protein sequences with the aid of Bleakley-Yamanishi Normalized Smith-Waterman Similarity Score.

Maximal Unbiased Benchmarking Datasets for human Chemokine Receptors Family

A tool to take a small molecule and generate new variants with enhanced properties.

MPhil thesis for Yang Zhang entitled "Simulation of protein dynamics for mechanistic insight and drug design"

Script that enable researchers to parse through ChEMBL bioactivity reports in relation to a specific biological target and provides insight into some important for Computer-Aided Drug Design (CADD) features.

Here you could find all of my fun and real world problems using Machine learning and Artificial Intelligence.

Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic discovery.

Computational drug discovery pipeline targeting Alzheimer's Disease: Virtual screening, ADMET profiling, and molecular docking of natural inhibitors.

A lightweight computational drug discovery webapp (bioactivity predictor) built using flask.