glycoengineering — Claude Code skill: protein glycosylation analysis
A skill for working through N- and O-glycosylation sites in protein sequences: motif scanning, mutation planning and predictor prep.
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a claude-codeWhat glycoengineering does
The skill walks through glycosylation analysis for eukaryotic secretory-pathway proteins. It starts by recording the accession, isoform, exact sequence, expression host and signal peptide topology. Canonical N-X-[S/T] candidates are then scanned with X not proline, and overlapping hits are kept: in NNST a candidate begins at position 1 and another at position 2. S/T-rich stretches get a separate pass for mucin-type O-GalNAc, though density there is a descriptive feature only, not a probability of glycosylation.
A local helper ships as scripts/glycoengineering_tools.py and uses the Python standard library. It takes sequences of the 20 canonical amino acids, normalizes case and whitespace, and rejects FASTA headers, gaps and unknown residues. The functions find_n_glycosylation_sequons, eliminate_glycosite, add_glycosite and find_st_rich_sites report 1-based coordinates against the sequence you submitted. Put the scripts/ directory on PYTHONPATH, or run Python from inside it.
Predictions go through the official web forms for NetNGlyc 1.0 and NetOGlyc 4.0. There is no stable submission API or job-polling endpoint here, so keep input, output and service version together. The local helpers need Python 3.10+. GlyTouCan lookup uses requests and network access. Structural glycan shielding calls for a separate GlycoSHIELD install with glycan libraries and GROMACS for SASA analysis; without those the step will not run.
What it helps with
- scan a protein sequence for canonical N-glycosylation sites
- knock out one glycosylation site with a point substitution
- introduce a new N-X-[S/T] site and list every residue changed
- flag S/T-rich regions before O-GalNAc triage
- compare antibody glycoforms by site occupancy
Example prompts for the agent
- Scan this sequence for canonical N-glycosylation sites and list their positions
- Remove the site at position 1 with a Q substitution and check for overlapping motifs
- Find S/T-rich regions in this sequence and tell me what to check next
How to install glycoengineering
1Skills CLI (Vercel)
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a claude-code2Manually: put the files in place
~/.claude/skills/glycoengineering/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/glycoengineering/
1Skills CLI (Vercel)
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a codex2Manually: put the files in place
.agents/skills/glycoengineering/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a cursor2Manually: put the files in place
.cursor/skills/glycoengineering/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install K-Dense-AI/scientific-agent-skills glycoengineering2Manually: put the files in place
.github/skills/glycoengineering/SKILL.md1Skills CLI (Vercel)
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a gemini-cli2Platform CLI
gemini skills install https://github.com/K-Dense-AI/scientific-agent-skills --path skills/glycoengineeringManually: put the files in place
.devin/skills/glycoengineering/SKILL.mdThe legacy .windsurf/skills/ path still works
Skills CLI (Vercel)
npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a opencodeClaude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: How to install skills in Claude Code: five ways
Questions about glycoengineering
How do I install glycoengineering in Claude Code?
Run npx skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering -a claude-code. The skill lands in ~/.claude/skills/glycoengineering/SKILL.md.
What does glycoengineering do?
It scans for N-glycosylation sites and S/T-rich regions, plans point mutations with a motif rescan, and prepares input for NetNGlyc, NetOGlyc and GlycoSHIELD.
What do the local functions need?
Python 3.10+ and the scripts/ directory on PYTHONPATH. GlyTouCan lookup also needs requests and network access.
