README.md

---
license: mit
language:
- en
tags:
- carbohydrate
- molecular dynamics
pretty_name: Glycoshape
viewer: true
configs:
- config_name: default
  data_files:
  - split: raw
    path: data/glycoshape_data.csv
---

# GlycoShape: A structural dataset of glycans


GlycoShape is a curated dataset of carbohydrate conformational ensembles derived from molecular dynamics simulations and structural analysis. 
The dataset aims to provide standardized structural representations of glycans and glycosidic torsions to support computational glycobiology, 
structural bioinformatics, and machine learning applications.

The dataset provides torsional information, conformational clusters, and representative structures for glycan fragments. 
It is designed to facilitate research on glycan conformational landscapes, glycosidic linkage preferences, and carbohydrate–protein recognition.

---

## Dataset Description

>  A gift to Rosetta Commons. 

Carbohydrates exhibit complex conformational behavior due to the flexibility of glycosidic bonds. Understanding these conformations is essential for studying:

  - **glycan recognition by proteins**
  
  - **carbohydrate-binding specificity**
    
  - **glycan structural motifs**

  - **glyco-bioinformatics and machine learning models**
  
  
GlycoShape (source: [glycoshape.org](https://glycoshape.org/)) provides curated conformational ensembles with standardized torsion angle annotations and clustering results.
The dataset contains glycosidic torsion trajectories and cluster assignments extracted from MD simulations and processed into easily usable tabular formats.

---

## Dataset Reproduction

Primary clustered structures were downloaded in :

    https://glycoshape.org/downloads

Secondary clustered structures were downloaded via : 

    $ python ./src/secondary_cluster_fetch.py
    
Torsion tables of secondary clustered structure were fetched via : 

    $ python ./src/fetch_torsion.py

The metadata table was generated via:

    $ python ./src/data_extract.py

---

## Dataset Fields

The MD structural files after primary clustering is in [./raw_data](https://huggingface.co/datasets/Jacky233emm/GlycoShape/tree/main/raw_data)

The MD structural files after seconday clustering is in [./clustered_data.zip](https://huggingface.co/datasets/Jacky233emm/GlycoShape/blob/main/clustered_data.zip)

The metadata is in [glycoshape_data.csv]('https://huggingface.co/datasets/Jacky233emm/GlycoShape/blob/main/data/glycoshape_data.csv') includes: 

| Field | Description |
|---|---|
| 'SNFG' | figure of Symbol Nomenclature for Glycans (SNFG) |
| 'torsion_table' | raw table of glycosidic bond torsions of glycan from MD simulation |
| 'torsion_analysis' | analysis of glycosidic bond torsions of glycan from MD simulation  |
| 'glytoucan' | glytoucan ID |
| 'ID' | GlycoShape ID |
| 'name' | glycan name |
| 'glycam' | name in GLYCAM format |
| 'iupac' | name in IUPAC format |
| 'iupac_extended' | name in extended IUPAC format|
| 'wurcs' | name in extended WURCS |
| 'glycoct' | name in GLYCOCT |
| 'smiles' | SMILES format |
| 'oxford' | name in Oxford glycan notation system |
| 'mass' | molecular mass |
| 'motifs' | involving glycan motifs |
| 'termini' | termini monosaccharide unit |
| 'components' | monosaccharide components  |
| 'composition' | monosaccharide composition  |
| 'rot_bonds' | Number of Rotatable Bonds |
| 'hbond_donor' | Number of Hydrogen Bond Donors |
| 'hbond_acceptor' | Number of Hydrogen Bond Acceptors |
| 'entropy' | conformational entropy quantifies the degree of structural flexibility of the glycan, It measures how widely distributed the conformational ensemble is across clusters. |
| 'clusters' | the percentage of simulation frames that fall into seondary 5 conformational clusters |
| 'coverage_clusters' | the percentage of simulation frames that fall into primary conformational clusters according to torsions |
| 'silhouette_scores' | average silhouette score obtained for different numbers of clusters (k) during the secondary clustering  |
| 'coverage_clusters_per_main' | a hierarchical grouping of the primary conformational clusters into 5 secondary cluster |
| 'pca_variance' | information of PCA analysis according to torsions |
| 'length' | MD simulation Length (μs) |
| 'package' | MD Engine |
| 'forcefield' | MD Force Field |
| 'temperature' | MD Temperature (K) |
| 'pressure' | MD Pressure (bar) |
| 'salt' | MD Salt (mM) |
| 'a_glycam' | GLYCAM ID of alpha anomer |
| 'a_iupac' | IUPAC of alpha anomer |
| 'a_iupac_extended' | extended IUPAC of alpha anomer |
| 'a_glytoucan' | Glytocan ID of beta anomer |
| 'a_wurcs' | WURCS iD of beta anomer |
| 'b_glycam' | GLYCAM ID of beta anomer |
| 'b_iupac' | IUPAC of beta anomer |
| 'b_iupac_extended' | extended IUPAC of beta anomer |
| 'b_glytoucan' | Glytocan ID of beta anomer |
| 'b_wurcs' | WURCS iD of beta anomer |
| 'common_names' | common name |
| 'description' | description |
| 'keywords' | keywords |
| 'calculated_torsion' | torsion information of archetype calculated from secondary clustered structure |
| 'a_calculated_torsion' | torsion information of alpha anomer calculated from secondary clustered structure |
| 'b_calculated_torsion' | torsion information of beta anomer calculated from secondary clustered structure |
| 'glycosmos' | organismal annotations from GlyCosmos |
| 'number_monosaccharides' | monosaccharide count |
| 'species' | organismal annotations from glygen |
| 'classification' | classifications |
| 'enzyme' | related enzyme |
| 'crossref' | reference |
| 'mass_pme' | Permethylated Mass |
| 'tool_support' | supporting tool |
| 'missing_score' | degree of missing structural information or incomplete sampling in the conformational dataset |
| 'glycan_type' | type of glycan |
| 'byonic' | glycan composition and theoretical mass used in glycoproteomics mass-spectrometry |
| 'gwb' | GlycoWorkbench format. |
| 'motifs' | glycan motif in GlycoMotif (GGM) database |
| 'subsumption' | subsumption relationships of this glycan within the GlyTouCan / GNOME glycan ontology hierarchy. |
| 'section_stats' | biological annotations |
| 'history' | version history in glycoshape |


---
## Citation
Ives, C.M., Singh, O. et al. Restoring protein glycosylation with GlycoShape. Nat Methods (2024).

## Licensing

All of the data provided is freely available for use under Creative Commons Attribution 4.0  (CC BY 4.0 Deed) licence terms

---

## Dataset Card Authors

Yijie (Jacky) Luo : jacky233@163.com; 

Ming Shen : mingshen01@gmail.com;

Kaley Chinoy : chinoykaley@gmail.com.