Error code:   JWTInvalidSignature
Exception:    InvalidSignatureError
Message:      Signature verification failed
Traceback:    Traceback (most recent call last):
                File "/src/libs/libapi/src/libapi/jwt_token.py", line 286, in validate_jwt
                  decoded = jwt.decode(
                      jwt=token,
                  ...<2 lines>...
                      options=options,
                  )
                File "/usr/local/lib/python3.14/site-packages/jwt/api_jwt.py", line 368, in decode
                  decoded = self.decode_complete(
                      jwt,
                  ...<8 lines>...
                      leeway=leeway,
                  )
                File "/usr/local/lib/python3.14/site-packages/jwt/api_jwt.py", line 265, in decode_complete
                  decoded = self._jws.decode_complete(
                      jwt,
                  ...<3 lines>...
                      detached_payload=detached_payload,
                  )
                File "/usr/local/lib/python3.14/site-packages/jwt/api_jws.py", line 270, in decode_complete
                  self._verify_signature(
                  ~~~~~~~~~~~~~~~~~~~~~~^
                      signing_input,
                      ^^^^^^^^^^^^^^
                  ...<4 lines>...
                      options=merged_options,
                      ^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/usr/local/lib/python3.14/site-packages/jwt/api_jws.py", line 417, in _verify_signature
                  raise InvalidSignatureError("Signature verification failed")
              jwt.exceptions.InvalidSignatureError: Signature verification failed

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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 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)

Dataset Curator/Dataset Card Author

Elijah Day (ehday@ucla.edu)

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Total file size:

1.69 MB

Collection including RosettaCommons/PRIDE_Crosslinking_Archive

Rosetta Data Bazaar

Collection

Experimental and simulated molecular datasets • 24 items • Updated Mar 20 • 2