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AlphaFold

A practical guide

    • Course overview
    • Search within this course
    • An introductory guide to AlphaFold’s strengths and limitations
      • What are proteins and how do we know their structures?
      • What is the protein folding problem?
      • What is AlphaFold?
      • Strengths and limitations of AlphaFold 2
      • Test your knowledge
    • Validation and impact
      • How have AlphaFold2’s predictions of protein structure been validated?
      • How accurate are AlphaFold 2 structure predictions?
      • How is AlphaFold 2 used by scientists?
    • Inputs and outputs
      • AlphaFold2: A high-level overview
      • Evaluating AlphaFold2’s predicted structures using confidence scores
        • pLDDT: Understanding local confidence
        • PAE: A measure of global confidence in AlphaFold2 predictions
        • Confidence scores in AlphaFold-Multimer
      • AlphaFold2 inputs and outputs – Recap
      • Other tools to check quality of the predicted structures
    • Accessing and predicting protein structures with AlphaFold 2
      • Choosing how to access AlphaFold2
      • Accessing predicted protein structures in the AlphaFold Database
        • What’s the best way to access the database?
        • Using the AlphaFold database for analysis
          • Navigating the structural landscape
      • Predicting protein structures with ColabFold and AlphaFold2 Colab
      • Predicting protein structures using the AlphaFold2 open-source code
      • Other ways to access predicted protein structures
      • How to cite AlphaFold
    • Advanced modelling and applications of predicted protein structures
      • Customising AlphaFold2 structure predictions
        • Outputs from ColabFold
      • Using AlphaFold2 predicted structures to tackle deeper questions
      • Enhancements to AlphaFold2 from the wider scientific community
    • Classifying the effects of missense variants using AlphaMissense
      • Introducing missense variants and AlphaMissense
      • Understanding pathogenicity scores from AlphaMissense
      • AlphaMissense in the AlphaFold Database
    • AlphaFold 3 and AlphaFold Server
      • Introducing AlphaFold 3
        • How does AlphaFold 3 work?
        • What AlphaFold 3 struggles with
        • Should I use AlphaFold 2 or AlphaFold 3?
        • How have AlphaFold 3’s predictions been validated?
      • AlphaFold Server: Your gateway to AlphaFold 3
        • A step-by-step guide to generating predictions with AlphaFold Server
        • Advanced features of AlphaFold Server
        • Interpreting results from AlphaFold Server
      • How to assess the quality of AlphaFold 3 predictions
      • Using the AlphaFold 3 source code
    • Summary
    • Course slides
    • Your feedback
    • Glossary of terms
    • Acknowledgements

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