BindingDB for Computational Drug Discovery: From Experimental Affinity Data to ML and Docking Benchmarks
BindingDB stores measured affinities. Michael Gilson's first BindingDB webinar is a guide to which rows can supervise a docking or machine-learning job, and which lookalikes cannot.
Aug 2, 2026
Learn CADD
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
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.
Feb 4, 2025
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.
Oct 23, 2024
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.
Sep 28, 2024
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.
Jun 16, 2024
Energy Minimization with Open Babel: Practical Guide for Ligand Preparation
Step-by-step workflow for energy minimization of ligands using Open Babel’s obminimize tool, with comparisons of force fields and minimization algorithms for docking and molecular modeling.
Jan 12, 2024