Structural Biology — Data Braids

Four datasets anchoring protein structure and function analysis. All ingested on westGate through the full Provenance Trio pipeline.

PDB mmCIF (full mirror)

Complete Protein Data Bank mirror in mmCIF format. 257K experimentally determined 3D structures of proteins, nucleic acids, and complex assemblies resolved by X-ray crystallography, cryo-EM, and NMR.

The Braid

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

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:pdb-mmcif-westgate-20260730",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "rsync://rsync.rcsb.org/ftp_data/structures/divided/mmCIF/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-07-30T...",
  "eco:license": "CC0-1.0",
  "eco:blake3_root": "...",
  "eco:file_count": 257179,
  "eco:size_bytes": 94489280512
}

What’s Possible

• Cross-reference with ChEMBL 37 binding data for structure-activity analysis
• Feed neuralSpring for structure prediction validation against experimental structures
• Combine with UniProt Swiss-Prot for function-structure mapping across the proteome
• Input for hotSpring molecular dynamics simulations on sovereign hardware

UniProt Swiss-Prot

570K+ manually curated and reviewed protein sequence entries with functional annotations, post-translational modifications, and cross-references to 180+ external databases.

What’s Possible

• Map tissue-specific expression (GTEx V8) to protein function annotations
• Combine with PDB for sequence-structure-function triangulation
• Feed wetSpring evolutionary analysis with curated functional context

The Braid

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

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:uniprot-swissprot-westgate-20260729",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/",
    "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": 3,
  "eco:size_bytes": 801112064
}

UniProt TrEMBL (unreviewed)

251M+ unreviewed protein sequences from automated annotation. Complete proteome coverage for computational biology workflows.

What’s Possible

• Massive sequence space for homology searches across all known life
• Combine with UniRef90 for clustered analysis at different identity thresholds
• Feed neuralSpring for structure prediction at scale

The Braid

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

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:uniprot-trembl-westgate-20260801",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-08-01T...",
  "eco:license": "CC-BY-4.0",
  "eco:blake3_root": "...",
  "eco:file_count": 3,
  "eco:size_bytes": 158913789952
}

PDB70 HHblits database

PDB70 clustered at 70% sequence identity for HHblits remote homology detection. Template-based structure prediction and profile-profile alignment.

What’s Possible

• Template detection for neuralSpring structure prediction
• Combine with PDB mmCIF for full template-based modeling pipeline
• Remote homology detection for proteins with no close PDB match

The Braid

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

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:pdb70-westgate-20260801",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-08-01T...",
  "eco:license": "CC-BY-SA-4.0",
  "eco:blake3_root": "...",
  "eco:file_count": 4,
  "eco:size_bytes": 28991029248
}

See Also

• Data Braids Index — all datasets
• Proteomics — UniRef90, PDB structures (complementary)
• Drug Discovery — ChEMBL, PubChem (cross-reference targets)