Site Confidence Scores for Protein Cross-Links Across All Available Structures

A confidence score for cross-linked peptides in the XLinkDB database, combining solvent-accessible surface distance, solvent accessibility, and salt bridge information. The dataset, authored by Andrew Keller and updated in April 2026, reveals that 12% of cross-links in XLinkDB lack high-confidence PDB structures. It is provided as a 24.9 KB Excel file.

Use Cases

• Assess the likelihood of a cross-link originating from specific protein structures based on combined distance, accessibility, and salt bridge scores.
• Identify cross-links that can serve as biomarkers for particular protein conformational states, as demonstrated with ADP/ATP translocase.
• Prioritize cross-links for additional structural modeling where existing PDB structures yield low confidence scores.

Strengths

• Integrates three distinct biophysical factors (SASD, solvent accessibility, salt bridges) into a single confidence metric.
• Demonstrated utility for state-specific biomarker identification in a case study.
• Identifies a specific subset (12%) of cross-links that may inform new structure prediction.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is very small (24.9 KB), indicating limited scope.

Provenance

Source

Andrew Keller, via the public cross-linking database XLinkDB.

Collection Method

Scores derived from combining structural data (PDB) with cross-link information.

Time Range

null

Freshness

Last updated 2026-04-21 19:36:24; freshness should be verified.

Geography

null