Analyzes protein 3D structures, performs homology modeling, interprets AlphaFold predictions, conducts molecular docking, and evaluates protein-ligand interactions; trigger when users ask about PDB files, folding, binding sites, or structural biology.
Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.