alterlab-alphafold

# AlphaFold (via ColabFold) ## Overview Predict a protein's 3D structure from its amino-acid sequence with **AlphaFold2**, run through **ColabFold** (Mirdita et al., *Nature Methods* 2022) — which replaces AlphaFold's slow genetic-database MSA search with the fast **MMseqs2** API, making folding practical on a single GPU. Handles single chains (monomer) and complexes via **AlphaFold2-Multimer** (Evans et al. 2021), and reports per-residue and per-interface **confidence metrics** so you know which parts of a prediction to trust. This skill **runs** folding and returns structures + confidence. To retrieve an *already-computed* AlphaFold prediction for a known UniProt entry without running anything, use `alterlab-alphafold-db` instead. ## When to Use This Skill Use this skill when the user wants to: - Fold a protein sequence (FASTA) into a predicted 3D structure (PDB/mmCIF). - Predict a protein **complex** (AF2-Multimer) and score the interface (ipTM). - Rank multiple models and read confidence (pLDDT, pTM, PAE) to judge reliability. - Validate a designed sequence by refolding it and checking self-consistency vs. a target. ### Does NOT Trigger | Scenario | Use instead | |----------|-------------| | Co-fold a protein **with a ligand** (SMILES/CCD) or predict binding affinity | `alterlab-boltz` | | Antibody–antigen / arbitrary multi-entity complex from one FASTA | `alterlab-chai` | | Look up a **precomputed** AlphaFold model by UniProt id | `alterlab-alphafold-db` | | ESM e...