Drug Discovery

Limitations of scale-based evaluation in structural biology, and the transition toward physical grounding, out-of-distribution generalization, and biophysical developability validation.

Jul 21, 2026

A practical map of protein and protein-ligand descriptors for machine learning modeling, from sequence-only features to MD-derived structural and interaction features.

Jul 20, 2026

An open-access registry, selection wizard, and interactive benchmark dashboard for chemical and biological vector representations. Indexes foundation models across five modalities: small molecules, proteins, complexes, chemical reactions, and nucleic acids, with a programmatic JSON API.

Jul 16, 2026

Limitations of static single-structure docking for flexible targets, and an integrated workflow combining molecular dynamics, clustering, and machine learning.

Jul 5, 2026

An interactive, visual, first-principles web guide to computer-aided drug design. Covers 18 modules across ligand-receptor binding, molecular docking, pharmacophore modeling, QSAR, molecular dynamics, generative design, and ADMET prediction, each with hands-on browser playgrounds.

Jun 24, 2026

A pipeline I never wrote a line of worked flawlessly on the first try, and it left me with impostor syndrome. Here is why relying on AI agents is not cheating, but a permanent shift in what scientific expertise actually means.

Jun 23, 2026

Pinning random_state=42 makes a UMAP-based train/test split perfectly reproducible - and that is exactly why it can lull you into a false sense of rigor. Reproducibility guarantees you get the same answer every run; it says nothing about whether that answer is typical. Here's the distinction, why it matters for evaluating GNNs on chemical-domain shifts, and how to fix it.

Jun 23, 2026

Partial charges quietly drive the electrostatics behind every docking score. This guide compares the common semi-empirical options - AM1-BCC, PM6, AM1/PM3, Gasteiger and RESP - and gives a practical recommendation for when to use each.

Jun 23, 2026

A step-by-step, fully open-source pipeline that turns raw Protein Data Bank structures into a ligand-based 3D pharmacophore - mining the PDB, aligning binding pockets, clustering ligands, fixing bond orders, and distilling a consensus feature map ready for virtual screening.

Jun 23, 2026

AI in drug discovery is moving past one-shot predictions toward autonomous agents that plan experiments, write their own analysis code, call docking and QM tools, and critique their results. Here's what the shift means, the design patterns behind it, and five open-source agents worth examining - with an honest look at the caveats.

Jun 23, 2026