# Glycobiology

Glycosylation site prediction and glycobiology analysis.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Data and ML
- License: MIT license
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill glycobiology -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill glycobiology -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill glycobiology -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill glycobiology -g -a gemini-cli -y`

## Description

Glycosylation site prediction and glycobiology analysis. N-glycosylation motif finding, O-glycosylation hotspot prediction, glycan structure resources. Lightweight, pure Python. For protein function queries use uniprot-database; for structure analysis use alphafold-database.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Glycobiology: Glycosylation Analysis

## Overview

Glycobiology provides lightweight computational tools for predicting and analyzing glycosylation sites in protein sequences. This skill covers N-glycosylation sequon motif finding (N-X-S/T where X is not P), O-glycosylation hotspot prediction using a sliding window serine/threonine density heuristic, glycan structure tool references, and combined glycoprotein analysis with domain mapping. All analyses use pure Python with minimal dependencies (Biopython for sequence I/O, regex for pattern matching).

## When to Use This Skill

- Predicting N-glycosylation sites from protein sequences
- Identifying O-glycosylation hotspot regions
- Planning glycosylation site mutagenesis experiments
- Comparing predicted vs experimentally determined glycosylation sites
- Annotating glycosylation in biotherapeutic protein design
- Surveying glycan analysis tools for downstream structural studies

**Related Skills:** For protein function and existing glycosylation annotations use `uniprot-database`. For protein 3D structure and site accessibility use `alphafold-database`. For sequence manipulation use `biopython`.

## Installation

```bash
uv pip install biopython numpy
```

No additional dependencies required, this skill uses pure Python.

## Quick Start

```python
import re

def find_n_glycosylation_sites(sequence):
    """Find N-X-S/T sequons where X != P."""
    sites = []
    for i in range(len(sequence) - 2):
        if sequence[i] == 'N' and sequence[i+1] != 'P' and sequence[i+2] in ('S', 'T'):
            sites.append({
                'position': i + 1,  # 1-based
                'motif': sequence[i:i+3],
                'context': sequence[max(0,i-3):i+6]
            })
    return sites

# Example: human EPO
epo_seq = "MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPDTKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR"

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/glycobiology/SKILL.md