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alphafold

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Use when running AlphaFold2 predictions on custom protein sequences, validating designed sequences via self-consistency, predicting binder-target complexes, or interpreting AF2 confidence metrics (pLDDT, pTM, ipTM).

skills/alphafold/SKILL.md

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# AlphaFold2 Structure Prediction

Use when the agent needs to run AlphaFold2 for protein structure prediction and complex modeling. Covers validating designed sequences, predicting binder-target complexes, and calculating confidence metrics (pLDDT, pTM, ipTM).

Distinct from `alphafold-database` (which retrieves pre-computed structures) — this skill covers running AF2 predictions on custom sequences.

## Requirements

- Python 3.8+
- CUDA 11.0+, 32 GB GPU VRAM minimum (A100 recommended)
- For multimers: ColabFold recommended over local install

## Deployment Options