antibody-engineering
Number antibody variable domains, annotate CDRs, and assess developability from sequence. Use this skill to apply IMGT, Kabat, Chothia, Martin, or AHo numbering with ANARCI, delimit CDRs and framework regions, scan for chemical liabilities (N-glycosylation sequons, deamidation NG, isomerisation DG, oxidation, unpaired cysteine, fragmentation), compute pI, net charge, extinction coefficient and hydrophobicity, and plan humanisation by CDR grafting. Also trigger on antibody, nanobody, VHH, scFv, Fab, CDR, framework, ANARCI, abnumber, IgBLAST, OAS, SAbDab, humanization, Vernier residues, or developability.
- Version
- 1.0
- License
- MIT
- Compatibility
- scan_liabilities.py and physchem_profile.py need only Python 3.10+ and the standard library. number_antibody.py additionally needs anarci (pip install anarci) and HMMER with hmmscan on PATH (conda install -c bioconda hmmer, or brew install hmmer). No GPU, no network, no API key.
Pinned to revision f67572246d9b, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/antibody-engineering/SKILL.md
- skills/antibody-engineering/references/developability.md
- skills/antibody-engineering/references/humanization-and-design.md
- skills/antibody-engineering/references/numbering-schemes.md
- skills/antibody-engineering/references/tools.md
- skills/antibody-engineering/scripts/number_antibody.py
- skills/antibody-engineering/scripts/physchem_profile.py
- skills/antibody-engineering/scripts/scan_liabilities.py
Every link opens the file at its source, pinned to the revision this page describes.