Complete tutorial in simple terms

How to predict protein structures with AlphaFold 2 using ColabFold

Because many readers reach out asking about this, here’s a guide to AlphaFold including a straightforward introduction and how to run it through ColabFold including ways to model multimers, employ custom templates, and interpret 1D and 2D confidence metrics -all kept simple and with a real-life example.

Article by a former CASP assessor who uses molecular modeling and simulations in its work at EPFL. To see more technical articles, check this index.

Introduction

The structure of a protein, that is the spatial disposition of all its atoms, determines its function, interaction with other molecules, regulation, stability, and all other kinds of relevant properties. Knowing a protein’s structure is therefore essential to understand how it works, how we can block or activate its activity with a drug, how we can tune its function or stability for a biotechnological application, etc. That’s all relevant as fundamental knowledge and for applications in medicine and processes.

Protein structure modeling is the process of predicting the three-dimensional structure of a protein (the “target” protein) from its amino acid sequence. Methods for…