- Course overview
- Search within this course
- An introductory guide to AlphaFold’s strengths and limitations
- Validation and impact
- Inputs and outputs
- Advanced modelling and applications of predicted protein structures
- Classifying the effects of missense variants using AlphaMissense
- AlphaFold 3 and AlphaFold Server
- Summary
- Course slides
- Your feedback
- Glossary of terms
- References
- Acknowledgements
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Using the AlphaFold database for analysis
This section explores how the AlphaFold Database (AFDB) can be used to analyse protein structures and their relationships. We’ll delve into two powerful features: clustering and Foldseek.
By the end of this section, you will be able to:
- Understand how proteins are clustered in the AFDB based on sequence and structural similarity.
- Access and interpret cluster information to gain insights into protein function and evolution.
- Perform structure-based searches using Foldseek to identify proteins with similar folds, even with low sequence similarity.
- Interpret Foldseek results, including E-values and RMSD values, to assess structural similarity.