Individual skill
protein-structure-prediction
Predicting protein structures with AlphaFold/ESMFold — setup, confidence assessment, and honest interpretation.
skills/protein-structure-prediction/SKILL.md
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## Overview
protein-structure-prediction covers modern AI-based structure prediction (AlphaFold2/3,
ESMFold, RoseTTAFold): running predictions, interpreting confidence metrics (pLDDT, PAE),
and knowing what predicted structures can and cannot tell you. Predicted structures are
models with quantified uncertainty — the confidence metrics are as important as the
coordinates.
## When to use
- Predicting structures: AlphaFold2 (monomer gold standard), AlphaFold3 (complexes,
ligands), ESMFold (fast, no MSA needed).
- Interpreting confidence: pLDDT per residue, PAE for domain orientation.
- Multimer/complex prediction and interface assessment.