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alphafold

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

When to use

• Validating designed sequences fold correctly
• Predicting binder-target complex structures
• Calculating confidence metrics (pLDDT, pTM, ipTM)
• Self-consistency validation of designs
• Multi-chain complex prediction with AlphaFold-Multimer

When not to use

• Faster single-chain prediction
• QC thresholds

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