From the author
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.
Install
npx skills add adaptyvbio/protein-design-skills --skill chai -a claude-code
Installs to .claude/skills/chai/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
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Why 80
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- boltzaipoch/open-scienceStructure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.Science★ 5.4K
- alphafoldadaptyvbio/protein-design-skillsValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.Science★ 170
- alterlab-chaiAlterLab-IEU/AlterLab-Academic-SkillsPredict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.Science★ 78
- esmaiskillstore/marketplaceComprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.Design★ 443
- protenixadaptyvbio/protein-design-skillsStructure prediction with Protenix, an open AlphaFold3 reproduction. Use this skill when: (1) Predicting complex structures with an AF3-class model, (2) Wanting an open alternative to AF3 alongside Boltz and Chai, (3) Validating designed binder-target complexes. For QC thresholds, use protein-qc. For ipSAE ranking, use ipsae.Science★ 170
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