README.md

---
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
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    num_examples: 17264
  - name: XL_intra
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    num_examples: 57774
  - name: XL_Alkyne_BVSC
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    num_examples: 80
  - name: XL_BS3
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    num_examples: 3793
  - name: XL_DSBU_d12
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    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
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    num_examples: 12610
  - name: XL_TTD
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    num_examples: 1374
  - name: XL_UCCL
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    num_examples: 2853
  - name: XL_VSD
    num_bytes: 287036
    num_examples: 3932
  - name: XL_VTT
    num_bytes: 214182
    num_examples: 2934
  download_size: 1683784
  dataset_size: 17106804
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 datasets

To load one of the `PRIDE_Crosslinking_Archive` datasets, use `datasets.load_dataset(...)`

    >>> dataset = datasets.load_dataset(
            path="RosettaCommons/PRIDE_Crosslinking_Archive",
            name="data",
            data_dir="data"
        )["XL_all"]
## Dataset Details

### Dataset Description
This dataset is a curated collection of crosslinking mass spectrometry (XL-MS) identifications sourced from PRIDE submissions and transformed into a consistent tabular format. Each record represents a single crosslink observation annotated with:
  * Crosslinking reagent(e.g., DSS/BS3/DSBU, etc.)
  * Crosslink type (inter-chain vs intra-chain)
  * UniProt Accession IDs for each crosslinked protein
  * Residue positions for the linked sites
  * For intra-chain crosslinks, Cα-Cα distance, calculated from AlphaFold Database structures

Alongside the full, merged table, the dataset includes inter/intra-chain splits, as well as per-crosslinker splits (one split per reagent). These splits should make it easy to analyze reagent-specific distance distributions and restraint behavior without additional filtering.

## Why AFDB distance mapping is included

A large fraction of downstream XL-MS analysis involves asking whether observed links are structurally plausible under a given model and/or what they imply about conformational states. By projecting intra-chain links onto AFDB structures, this dataset provides a standardized starting point for:

  * Comparing distance distributions across reagents

  * Identifying long-distance outliers that may indicate flexible regions or alternate conformations

  * Generating restraint sets for integrative modeling and benchmarking

## Uses
This dataset is intended to be used as a benchmark/calibration set for integrative modeling workflows. Included crosslinks can be used as a constraint set to evaluate predicted or refined models (AlphaFold/AlphaLink/integrative models) by measuring what fraction of links fall below chosen distance thresholds. 
Long-distance outliers in this dataset can also be used to identify proteins/protein families in which contemporary structure prediction methods fail to recapitulate experimental observations.

## Limitations
This dataset does not contain all of the identified crosslinks in the PRIDE repository. Only links with valid UniProt identifiers were included in this set.



### Source Data
Crosslinks were obtained from the PRIDE Crosslinking Archive ([PRIDE](https://www.ebi.ac.uk/pride/archive/crosslinking)) 

## Dataset Curator/Dataset Card Author
Elijah Day (ehday@ucla.edu)