Proteomics — Data Braids

Protein sequence clusters and high-priority structure targets for homology searches, MSA construction, and molecular dynamics.

UniRef90

Clustered protein sequences at 90% identity. Reduces redundancy while preserving diversity for homology searches and multiple sequence alignment construction. The standard reference for evolutionary covariance analysis.

What’s Possible

• Build multiple sequence alignments for structure prediction (neuralSpring)
• Feed evolutionary analysis pipelines (wetSpring)
• Cross-reference with PDB for template-based modeling
• Combine with UniProt Swiss-Prot for functional annotation of sequence clusters

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:uniref90-westgate-20260729",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-07-29T...",
  "eco:license": "CC-BY-4.0",
  "eco:blake3_root": "...",
  "eco:file_count": 1,
  "eco:size_bytes": 32212254720
}

PDB structures (506 individual)

506 individually retrieved PDB structures in PDB format. High-priority targets selected for molecular dynamics and structure prediction validation. Each file has its own CAS object and sweetGrass braid.

What’s Possible

• Direct input for hotSpring molecular dynamics simulations on sovereign hardware
• Validation targets for neuralSpring structure prediction
• Cross-reference with UniProt annotations for function assignment

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:pdb-structures-westgate-20260728",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://files.rcsb.org/download/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-07-28T...",
  "eco:license": "CC0-1.0",
  "eco:blake3_root": "...",
  "eco:file_count": 506,
  "eco:size_bytes": 378535936
}

See Also

• Structural Biology — PDB mmCIF mirror, UniProt (complementary)
• Gene Expression — GTEx tissue expression (protein context)