foundry-claude-skill

Foundry protein design toolkit reference. Auto-invoked when the user discusses protein design, structure prediction, inverse folding, RFdiffusion3, RosettaFold3, ProteinMPNN, LigandMPNN, SolubleMPNN, Enhanced MPNN, or running Foundry tools on GPUs.

Run ProteinMPNN, LigandMPNN, SolubleMPNN, or Enhanced MPNN sequence design on a Vast.ai GPU instance. Use when the user wants to design protein sequences for a given backbone structure, redesign sequences around ligands, optimize for solubility, or maximize designability.

Run RosettaFold3 structure prediction on a Vast.ai GPU instance. Use when the user wants to predict protein structures, validate designed sequences, fold protein-ligand complexes, or run RF3.

Run RFdiffusion3 protein design on a Vast.ai GPU instance. Use when the user wants to design protein binders, enzymes, symmetric assemblies, or any de novo protein structures using RFD3.

Run a complete Foundry protein design pipeline on Vast.ai: design with RFD3, sequence design with MPNN/Enhanced MPNN, and validate with RF3. Use when the user wants to run a multi-step protein design workflow or any foundry tool without specifying which one.