| --- |
| 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: 4316006 |
| num_examples: 57774 |
| - 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: 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) |
