Cheminformatics

Getting Started with Graph Neural Networks for Protein–Ligand Complexes Using DGL

A practical, beginner-friendly introduction to the Deep Graph Library (DGL) and how to use it to featurize protein–ligand complexes for machine learning in drug discovery.

Apr 5, 2026
What Agentic Engineering Means for Computational Drug Discovery

Simon Willison recently appeared on Lenny’s Podcast to discuss what he calls the November inflection point: the moment in late 2025 when frontier models crossed a threshold where agentic coding went from “mostly works if you watch carefully” to “almost always does what you asked.” His highlights post is worth reading in full, but reading it through the lens of computational drug discovery, several themes land with unusual force.

Apr 4, 2026
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
Understanding Binding Energetics in Molecular Docking

Conceptual overview of the key energetic contributions governing protein–ligand binding in molecular docking, including desolvation, entropy, water displacement, electrostatics, and scoring function behavior.

Mar 13, 2026
Practical System Preparation Tips for Molecular Dynamics Simulations

Preparing a molecular system correctly before running molecular dynamics (MD) simulations is essential for obtaining meaningful and reproducible results. Small technical choices such as solvent box geometry, treatment of protein termini, and strategies for selecting representative conformations can strongly influence simulation stability, computational efficiency, and interpretation of results.

Mar 9, 2026
How to Use DataWarrior for Drug Discovery: Key Workflows From the Villoutreix Tutorials

Practical introduction to DataWarrior as a free, chemistry-aware workbench for data visualization, filtering, and focused library generation, based on Bruno Villoutreix’s tutorial series.

Nov 15, 2025
AI + Chemistry: Building Drug Discovery Pipelines with Free Tools

Step-by-step guide to constructing an open-source drug discovery pipeline with AI and chemistry tools, from data to visualization.

Jul 1, 2025
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
How to build and validate 3D-QSAR models - Insights from Xu et al., 2020

Comprehensive, metric-driven workflow for robust 3D-QSAR modeling, based on Xu et al., 2020 and enriched with cheminformatics best practices.

Jan 13, 2024
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