A beginner-friendly walkthrough of PyTorch Geometric's point cloud tutorial — covering the Data object, transforms, dynamic graph construction, PointNet++ message passing, and graph-level classification.
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.
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.
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.
Conceptual overview of the key energetic contributions governing protein–ligand binding in molecular docking, including desolvation, entropy, water displacement, electrostatics, and scoring function behavior.
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.
A practical guide to the most common methodological errors in Density Functional Theory calculations, explaining why legacy protocols like B3LYP/6-31G* are no longer reliable and how to adopt robust, modern best practices.
A guide for researchers on avoiding common methodological errors in molecular dynamics, from structure preparation to force field selection and experimental validation.
A concise overview of how modern biotechnology, new therapeutic modalities, and smarter development strategies are transforming previously 'undruggable' targets into tractable opportunities.
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.
