bindcraft

Boltz provides open-source biomolecular structure prediction using Boltz-1/Boltz-2 models, serving as an alternative to AlphaFold2. It specializes in predicting protein complexes, validating designed binders, and handling protein-ligand interactions. This skill is particularly useful when you need open-source structure prediction or want to leverage local GPU resources.

The alphafold skill uses AlphaFold2 to validate protein designs by predicting structures and calculating confidence metrics. It supports single-chain validation, binder-target complexes, and multi-chain predictions with AlphaFold-Multimer. For faster single-chain predictions, developers should use the esm skill instead.

BoltzGen is an all-atom diffusion model for protein design that generates both backbone and side-chain coordinates simultaneously. It is particularly suited for designing proteins around small molecules or ligands where precise binding geometries are required. Use this skill when you need side-chain-aware design from the start and are working with a YAML-based configuration.

The alphafold skill uses AlphaFold2 to validate protein designs by predicting structures and calculating confidence metrics like pLDDT and pTM. It supports multi-chain complex prediction with AlphaFold-Multimer for validating binder-target interactions and design self-consistency. For faster single-chain predictions, developers should use the esm skill instead.