antibody-engineering

name	antibody-engineering
description	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.
license	MIT
allowed-tools	Read Write Edit Bash
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.
metadata	{"version":"1.0","skill-author":"K-Dense Inc.","openclaw":{"emoji":"🅨","homepage":"https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/"},"hermes":{"category":"research"}}

Antibody engineering

Sequence-level analysis for antibodies, nanobodies, and other variable-domain formats: numbering, CDR annotation, chemical liabilities, and physicochemical properties. All of it runs in seconds and rules out a surprising fraction of problems before a model or a wet-lab week is spent.

Read references/numbering-schemes.md before quoting any residue position, references/developability.md before acting on a liability, references/humanization-and-design.md for grafting and humanness, and references/tools.md for the wider ecosystem.

A residue number means nothing without its scheme

"Residue 52" is a different residue in IMGT, Kabat, and Chothia numbering, and the CDRs they define overlap only partially. The same trastuzumab heavy chain:

IMGT    CDRH1 GFNIKDTY (8)   CDRH2 IYPTNGYT (8)            CDRH3 SRWGGDGFYAMDY (13)
Kabat   CDRH1 DTYIH    (5)   CDRH2 RIYPTNGYTRYADSVKG (17)  CDRH3 WGGDGFYAMDY   (11)

Neither is wrong. Use IMGT by default — one definition for both chains, structurally principled gaps, and the germline database is IMGT-numbered — and convert to Kabat when matching legacy literature. State the scheme every time.

python skills/antibody-engineering/scripts/number_antibody.py antibody.fasta
python skills/antibody-engineering/scripts/number_antibody.py antibody.fasta --scheme kabat
python skills/antibody-engineering/scripts/number_antibody.py antibody.fasta \
    --format regions --out regions.tsv

# trastuzumab_VH: chain H, closest germline human_H (human), E=3e-60
#   variable domain spans input residues 1-120
  CDRH1	8	GFNIKDTY
  CDRH2	8	IYPTNGYT
  CDRH3	13	SRWGGDGFYAMDY

Needs pip install anarci plus HMMER (hmmscan on PATH). Note that ANARCI's species call is the closest germline, not an annotation — a humanised antibody reports human because its frameworks are human, which says nothing about its CDRs.

Liabilities, weighted by region

python skills/antibody-engineering/scripts/scan_liabilities.py antibody.fasta \
    --regions regions.tsv --min-severity high

# trastuzumab_VH: 120 residues, 3 finding(s)
  [critical] deamidation (NG) 'NG' at 55 (CDRH2)
             the fastest-deamidating motif; Asn -> iso-Asp/Asp changes charge and can
             abolish binding, and it is the usual cause of potency loss on storage
  [critical] isomerisation (DG) 'DG' at 102 (CDRH3)
             Asp-Gly isomerises to iso-Asp through a succinimide intermediate