# 4.5 Structure Prediction Landscape

> Structure Prediction Landscape (Module 4: The Bioinformatician's Toolkit). Key concept: AlphaFold & prediction tools. Explain what a structure predictor does, and what its confidence scores are actually scoring.

Structure Prediction Landscape (Module 4: The Bioinformatician's Toolkit). Key concept: AlphaFold & prediction tools. Explain what a structure predictor does, and what its confidence scores are actually scoring.

- Explain what a structure predictor does, and what its confidence scores are actually scoring
- Read pLDDT as per-residue confidence and identify which parts of a model to trust
- Read a PAE matrix to judge whether a domain–domain orientation is reliable
- Compare the current methods — AlphaFold2 as the MSA-driven workhorse, AlphaFold3 and its open successors, ESMFold for speed — and choose for the problem in front of you
- Recognise that low pLDDT often marks genuine disorder rather than a failed prediction
- Interrogate a prediction rather than accepting it

## Links

- [Module 4: The Bioinformatician's Toolkit](https://proteindesign.academy/module/4)
- [4.1 Reading a PDB File](https://proteindesign.academy/module/4/1)
- [4.2 Navigating a 3D Molecular Viewer](https://proteindesign.academy/module/4/2)
- [4.3 Sequence Alignments and BLAST](https://proteindesign.academy/module/4/3)
- [4.4 Evolutionary Conservation and ConSurf](https://proteindesign.academy/module/4/4)
- [The Structural Biologist](https://proteindesign.academy/module/4/capstone)