Beyond 2D Fingerprints: Encoding Protein-Ligand Interactions for Machine Learning
A practical guide to three advanced 3D fingerprinting methods (PLEC, SPLIF, and E3FP) and how to choose between them when featurizing docking poses for ML-based drug discovery models.
Apr 1, 2026
Computational Drug Repurposing with Multiscale Interactomes
A step-by-step workflow to identify repurposing candidates by integrating heterogeneous biomedical networks, graph embeddings, and experimental prioritization.
Apr 23, 2024
QSARBioPred
A Jupyter Notebook pipeline for building QSAR classification models for bioactivity prediction, supporting descriptor calculation, feature selection, model training, and applicability domain assessment.
Feb 20, 2024
EnsembleBBB
A machine learning ensemble model for predicting drug blood-brain barrier permeability, deployed as an interactive Streamlit web application for rapid compound screening.
Feb 13, 2024
Interpretable Machine Learning as a Key to Understanding BBB Permeability
Step-by-step tutorial on building an explainable ML model to predict blood-brain barrier permeability, using feature importance and SHAP analysis for interpretability.
Jan 23, 2024
Awesome Drug Discovery
A curated resource list of computational methods for drug discovery, covering molecular modeling tools, machine learning frameworks, databases, and open-source pipelines organized by application area.
Jan 16, 2024
Data-Driven Chemistry: How Data Science Empowers Drug Discovery
Exploring how data science techniques (from machine learning to data visualization) are transforming chemistry and accelerating the discovery of new drugs and materials.
Nov 8, 2023
Using PaDELPy to Generate Molecular Fingerprints for Machine Learning-Based QSAR
A step-by-step tutorial on using PaDELPy to calculate molecular fingerprints and build a Random Forest model for predicting molecular activity in drug discovery.
Mar 15, 2023
Supervised vs. Unsupervised Methods in Machine Learning
Overview of supervised and unsupervised learning approaches, highlighting key techniques, applications, and differences in the context of cheminformatics and drug discovery.
Oct 16, 2022
Chemical Databases Every ML Scientist Should Know for Drug Discovery
Overview of freely available chemical and bioactivity databases (ChEMBL, BindingDB, PubChem, PDBbind, and BRENDA) that fuel machine learning and cheminformatics research in drug discovery.
Sep 12, 2022