Tutorials, comparisons, and guides for molecular docking with AutoDock Vina, GNINA, and Glide.
How to Validate Molecular Docking Results: Redocking, Cross-Docking, and Benchmarking 16 min read Intermediate Running a docking calculation is easy. Knowing whether your results are trustworthy is hard — and it’s where most beginners stop short. This tutorial covers the full validation toolkit: why it matters, how to run self-docking validation step by step, how…
10 Common Molecular Docking Mistakes (And How to Avoid Every One) 13 min read All levels Most bad docking results don’t come from the algorithm — they come from avoidable preparation and interpretation errors that produce wrong answers without any error message. Here are the ten mistakes that appear most often in troubleshooting forums, paper…
GNINA Tutorial: Deep Learning Molecular Docking as an Alternative to AutoDock Vina 15 min read Intermediate GNINA does everything AutoDock Vina does — but replaces the scoring function with a convolutional neural network trained on millions of protein-ligand structures. The result is consistently better pose prediction with an almost identical workflow. This tutorial shows you…
Virtual Screening with AutoDock Vina: Screen a Compound Library Against a Protein Target 22 min read Intermediate Single-ligand docking is the proof of concept. Virtual screening is where docking becomes genuinely useful — filtering thousands of compounds down to a handful of experimentally testable hits. This tutorial walks through the complete pipeline: sourcing a library,…
How to Interpret Molecular Docking Results: Scores, Poses & What They Mean 13 min read Beginner to intermediate You’ve run AutoDock Vina and you’re staring at a table of scores. What does −8.3 kcal/mol actually mean? Is that good? How do you know if the pose is biologically meaningful? This guide explains exactly how to…
AutoDock Vina Tutorial for Beginners: Dock Your First Ligand From Scratch (2026) 22 min read Complete beginner By the end of this tutorial you will have run a complete molecular docking calculation — receptor prepared, ligand prepared, config file written, Vina executed, and results visualized. No prior experience with docking software required. Exact commands for…
How to Prepare a Protein for Molecular Docking: Complete Step-by-Step Guide 18 min read Beginner to intermediate Protein preparation is where most docking projects succeed or fail — and where most beginners spend the most time confused. A raw PDB file cannot go straight into AutoDock Vina. This guide walks through every step from downloading…
How to Install AutoDock Vina on Windows, Mac and Linux (2026 Guide) 12 min read Complete beginner AutoDock Vina is the most widely used free docking program in academic research — but the official documentation assumes you already know your way around a terminal. This guide doesn’t. Exact commands, what the output should look like,…
Free Molecular Docking Software in 2026: The Complete List 13 min read All levels You don’t need a Schrödinger license to do serious molecular docking. This guide covers every major free docking program worth knowing — what each one actually does, how to get it running, and which situations it’s best suited for. Contents At…
AutoDock vs AutoDock Vina vs Glide: Best Molecular Docking Software in 2026 15 min read Beginner to intermediate Three programs dominate molecular docking: AutoDock, AutoDock Vina, and Glide. They are not interchangeable — they make different accuracy-speed-cost tradeoffs, and the right choice depends entirely on what you’re trying to do. This is a no-hype comparison…