Blog

Molecular Docking

Choosing the Right Partial Charges for Molecular Docking: AM1-BCC, PM6 and Beyond

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.

Yassir Boulaamane

• Jun 23, 2026

Cheminformatics

Building a 3D Pharmacophore Model from PDB Data: A Free Python Workflow

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.

Yassir Boulaamane

• Jun 23, 2026

Artificial Intelligence

Beyond Static Models: Agentic AI and Multi-Agent Systems in Drug Discovery

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.

Yassir Boulaamane

• Jun 23, 2026

Machine Learning

Does data leakage really inflate binding-affinity GNNs? A laptop-scale reproduction

I tried to reproduce the well-known PDBbind data-leakage effect with a small 3D GNN on a laptop - and couldn't. Two independent diagnostics show why: leakage only inflates models strong enough to memorize.

Yassir Boulaamane

• Jun 19, 2026

GNN

A History of Graph Neural Networks in Drug Discovery

Graphs in drug discovery have gone from a quiet background tool to one of the main ways we think about molecules, proteins, and their interactions. This post walks through that story: how the field moved from fingerprints and QSAR to today’s 3D, attention-based graph neural networks operating directly on protein-ligand complexes.

Jun 8, 2026

QSAR

A Practical Guide to QSAR Model Validation: Internal, Cross, and External Checks

Building a QSAR model is only half the job. The harder question is: does it actually work? Overfitted models routinely pass internal checks while failing completely on new compounds. The OECD principles and decades of best-practice literature have converged on a three-tier validation framework that separates what a model has memorised from what it can genuinely predict.

Jun 1, 2026

Cheminformatics

Beyond SMILES: The Evolving Landscape of Molecular Representations

This post summarizes the key ideas from Zhang et al. (2026), “Molecular Knowledge Representations in the Era of Artificial Intelligence,” a preprint published on ChemRxiv (DOI: 10.26434/chemrxiv.15002830/v1). The Core Problem Molecules are quantum-mechanical objects. Their exact description is computationally intractable, and any real sample is a messy mixture of impurities, conformers, and side products. This means every representation of a molecule is, by necessity, an approximation - shaped by the interactions and length scales we care about.

May 23, 2026

Structural Biology

Choosing the Right PDB Structure: A Systematic Guide for Docking and MD Simulations

Your docking pose is only as trustworthy as your starting coordinates. Here is a systematic guide to navigating the PDB, avoiding common pitfalls, and future-proofing your workflow for the coming mmCIF era.

May 19, 2026

Computational Chemistry

Computational Strategies for Accelerating Drug Discovery: A Comprehensive Review

A comprehensive walkthrough of cheminformatics, machine learning, molecular docking, ADMET prediction, and molecular dynamics simulations as the modern toolbox for computer-aided drug discovery.

Yassir Boulaamane

• May 10, 2026

Deep Learning

Point Cloud Classification with Graph Neural Networks Using PyTorch Geometric

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.

Apr 5, 2026