| name | colabfold |
| description | Fast AlphaFold2/ColabFold protein structure prediction. Use when predicting monomer or multimer protein structures from FASTA, running colabfold_batch, interpreting pLDDT/PAE, or preparing predicted structures for docking, molecular dynamics, or publication figures. |
ColabFold
[!note] Vault audit 2026-07-24 — USE-11
Use this for local/batch AlphaFold2-style monomer or multimer folding from FASTA; for the hosted OpenFold NIMs use openfold2-nim (monomer) / openfold3-nim (complex), for local Boltz-2 use struct-predictor, and to just retrieve existing/AlphaFold DB structures use structural-biology. Local AF2 predict vs hosted NIM vs retrieve is the routing axis.
Use this skill for local or batch AlphaFold2-style protein structure prediction with ColabFold. It is especially useful when users need a familiar reference workflow, multimer predictions, or many FASTA sequences processed consistently.
Routing
- Use
struct-predictor when the task is about the vault's Boltz-oriented structure workflow.
- Use this skill when the user asks for AlphaFold2, ColabFold,
colabfold_batch, pLDDT, PAE, MSA generation, or protein complex prediction.
- Use
diffdock after structure prediction when the next step is ligand docking.
- Use
molecular-dynamics when the next step is relaxation, simulation, or trajectory analysis.
Batch Pattern
Input FASTA:
>protein_a
MSEQUENCE...
Run:
colabfold_batch input.fasta colabfold_out
For multimers, encode chains with : in the sequence or use the format supported by the installed ColabFold version.
Interpretation
- pLDDT: local confidence. Treat low-confidence loops/tails cautiously.
- PAE: domain-domain and chain-chain placement confidence.
- Ranking score: useful for triage, not a substitute for biological validation.
- Multimer interfaces require special scrutiny; inspect PAE and interface contacts.
Practical Checks
- Remove signal peptides, tags, or low-complexity tails only when biologically justified.
- Use the same FASTA identifiers across prediction, docking, and MD outputs.
- Keep all JSON/PAE outputs, not just the top PDB.
- For publications, report ColabFold version, model preset, database/MSA mode, and whether templates were used.
