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license: cc0-1.0
configs:
- config_name: data
data_files:
- split: XL_all
path: data/XL_all-*
- split: XL_inter
path: data/XL_inter-*
- split: XL_intra
path: data/XL_intra-*
- split: XL_Alkyne_BVSC
path: data/XL_Alkyne_BVSC-*
- split: XL_BS3
path: data/XL_BS3-*
- split: XL_DSBU_d12
path: data/XL_DSBU_d12-*
- split: XL_DSS
path: data/XL_DSS-*
- split: XL_DSSO
path: data/XL_DSSO-*
- split: XL_sulfo_SDA
path: data/XL_sulfo_SDA-*
- split: XL_TTD
path: data/XL_TTD-*
- split: XL_UCCL
path: data/XL_UCCL-*
- split: XL_VSD
path: data/XL_VSD-*
- split: XL_VTT
path: data/XL_VTT-*
dataset_info:
features:
- name: Data Source
dtype: string
- name: Crosslinker
dtype: string
- name: Accession A
dtype: string
- name: Accession B
dtype: string
- name: Residue A
dtype: int64
- name: Residue B
dtype: int64
- name: XL Type
dtype: string
- name: XL Distance
dtype: float64
splits:
- name: XL_all
num_bytes: 5702295
num_examples: 75038
- name: XL_inter
num_bytes: 1386289
num_examples: 17264
- name: XL_intra
num_bytes: 1386289
num_examples: 17264
- name: XL_Alkyne_BVSC
num_bytes: 6480
num_examples: 80
- name: XL_BS3
num_bytes: 278709
num_examples: 3793
- name: XL_DSBU_d12
num_bytes: 4446
num_examples: 57
- name: XL_DSS
num_bytes: 879796
num_examples: 12052
- name: XL_DSSO
num_bytes: 2720767
num_examples: 35352
- name: XL_sulfo_SDA
num_bytes: 996190
num_examples: 12610
- name: XL_TTD
num_bytes: 100302
num_examples: 1374
- name: XL_UCCL
num_bytes: 214306
num_examples: 2853
- name: XL_VSD
num_bytes: 287036
num_examples: 3932
- name: XL_VTT
num_bytes: 214182
num_examples: 2934
download_size: 1448868
dataset_size: 14177087
pretty_name: PRIDE Crosslinking Archive
---
# PRIDE Crosslinking Archive
<!-- Provide a quick summary of the dataset. -->
This dataset aggregates publicly available crosslinking mass spectrometry (XL-MS) datasets from the PRIDE repository.
Each dataset is curated and categorized by crosslinking reagent a link type (inter-chain vs intra-chain). For intra-chain links where the protein can be mapped to a
UniProt ID, each link is mapped onto the corresponding AlphaFold Database (AFDB) structure, and the Cα-Cα distance for the linked residue pair is reported.
The result is a standardized resource for analyzing XL-MS constraints across reagents and for benchmarking/evaluating integrative modeling pipelines.
## Quickstart Usage
### Install HuggingFace Datasets package
Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
First, from the command line install the `datasets` library
$ pip install datasets
Optionally set the cache directory, e.g.
$ HF_HOME=${HOME}/.cache/huggingface/
$ export HF_HOME
then, from within python load the datasets library
>>> import datasets
### Load model datasets
To load one of the `PRIDE_Crosslinking_Archive` datasets, use `datasets.load_dataset(...)` |