Protein Cross-Link Site Confidence Scores for Conformational Analysis

19.8 KB of cross-link site confidence scores added to the XLinkDB database. The dataset combines solvent-accessible surface distance, solvent accessibility, and salt bridge information to assess the likelihood of a cross-link originating from available protein structures. It was authored by Andrew Keller and last updated on April 21, 2026.

Use Cases

• Prioritizing cross-links for structural modeling based on the described composite confidence score.
• Identifying biomarkers for specific protein conformational states, as demonstrated with ADP/ATP translocase.
• Flagging cross-links that lack high-confidence structural matches for further modeling, as the description notes 12% of XLinkDB cross-links have no suitable PDB structures.

Strengths

• Provides a composite confidence score derived from three structural features (SASD, solvent accessibility, salt bridges).
• Demonstrated utility in a specific biological case study (ADP/ATP translocase).
• File is small (19.8 KB) and in a standard format (XLSX) for easy access.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The dataset's scope is limited to cross-links and structures within the XLinkDB database.

Provenance

Source

figshare, derived from the public cross-linking database XLinkDB.

Collection Method

Scores were calculated by combining structural metrics (SASD, solvent accessibility, salt bridge information).

Time Range

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Freshness

Last updated 2026-04-21 19:36:23; freshness should be verified.

Geography

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