How to Validate a Predicted Protein Structure Before Using It in Research 14 min read Intermediate A predicted protein structure — whether from AlphaFold, ESMFold, or a homology model — is a hypothesis, not a measurement. Validation is the process of testing that hypothesis before building your research on top of it. This article covers…
8 Common Mistakes When Using AlphaFold Structures in Research (And How to Avoid Every One) 12 min read All levels AlphaFold structures are easy to get and tempting to use immediately. The mistakes that follow are equally easy to make — and they appear regularly enough in submitted manuscripts that reviewers now have a standard…
How to Evaluate Protein Structure Quality: DOPE, QMEAN, MolProbity and Ramachandran Plots Explained 13 min read All levels Whether you’ve just built a homology model or downloaded an AlphaFold prediction, the next step before using any protein structure is the same: assess its quality. This guide explains every major quality metric, what it actually measures,…
AlphaFold-Multimer Tutorial: Predict Protein-Protein Interaction Structures with ColabFold 14 min read Intermediate Protein-protein interactions drive virtually every cellular process — but their 3D structures are notoriously hard to determine experimentally. AlphaFold-Multimer changed that. This tutorial covers what it does, when it’s the right tool, how to run it free with ColabFold, and — critically —…
How to Use an AlphaFold Structure for Molecular Dynamics Simulation 16 min read Intermediate AlphaFold structures can be simulated directly with GROMACS — but they need additional preparation steps that crystal structures don’t require. This tutorial covers everything from pLDDT assessment and handling disordered regions to running the simulation and validating results that reviewers will…
How to Use an AlphaFold Structure for Molecular Docking: Complete Workflow 18 min read Intermediate AlphaFold has made high-quality protein structures available for hundreds of millions of proteins — most of which have never been crystallized. This tutorial bridges the structure prediction and docking pillars: how to go from an AlphaFold prediction to a docking-ready…
AlphaFold vs Homology Modeling: When to Use Each 12 min read All levels AlphaFold didn’t make homology modeling obsolete — it made the choice between them more nuanced. Understanding when each method is genuinely better leads to better structures, fewer wasted experiments, and more defensible methods sections. Contents How they differ fundamentally When AlphaFold is…
Homology Modeling Tutorial: Swiss-Model and MODELLER for Beginners 16 min read Beginner Homology modeling has been the workhorse of structural biology for three decades — and despite AlphaFold’s emergence, it remains the method of choice in several important situations. This tutorial explains what it is, when to use it, and how to run it using…
How to Interpret AlphaFold Output: pLDDT Scores, PAE Plots and Model Quality 13 min read Beginner to intermediate Getting an AlphaFold prediction is easy. Knowing what to trust — and what to ignore — requires understanding two metrics that most tutorials mention but rarely explain: pLDDT and PAE. This article teaches you to read both,…
How to Use AlphaFold2 with ColabFold: Predict a Protein Structure for Free (2026 Guide) 15 min read Complete beginner ColabFold brings AlphaFold2-quality structure prediction to any researcher with a Google account — no installation, no HPC cluster, no cost. This tutorial walks through every step from opening the notebook to downloading and interpreting your results….