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
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 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(...)