AlphaFold2 (ColabFold runner)

This skill wraps AlphaFold2 and AlphaFold2-Multimer through colabfold_batch, which replaces DeepMind's local-database MSA pipeline with a call to the public MMseqs2 server — so a prediction is one command and one FASTA, not a 2 TB database mount. AF2 remains the reference monomer predictor and the multimer model is still a strong protein–protein validator, but it does not handle ligands or nucleic acids; for those, route to boltz, chai1, or openfold3. The ColabFold code is MIT (github.com/sokrypton/ColabFold) and the AlphaFold2 code is Apache-2.0 (github.com/google-deepmind/alphafold); the AF2 model parameters are CC-BY-4.0 with DeepMind's terms of use.

Running it

colabfold_batch input.fasta out \
  --num-recycle 3 \
  --model-type alphafold2_multimer_v3