Targets — browse / sort / filter (view)

Data license: CC BY 4.0 · Data source: apt-scout automated curation pipeline (E. Dohi, NCNP) — values harvested from public databases; raw source stored per target

id

UniProt accession (human). Links to uniprot.org.

gene_symbol

Gene symbol (e.g. ITGB3).

protein_name

Protein name (UniProt).

tier

Tier 1 = PDB-anchored; Tier 1.5 = AlphaFold-confident.

has_structure

1 if the target protein has a reported experimental 3D structure (PDB). This is the CORE requirement the aptamer-Kd layer is built around — filter to 1 for the structure-backed set.

evidence_priority

DETERMINISTIC, reproducible prioritisation (0-1) computed at build time from real harvested columns: 0.35*experimental-structure(PDB=1 / AlphaFold-only=0.3) + 0.30*Open-Targets-top-disease-score + 0.20*PREDICTED-surface-accessibility(A_surface=1) + 0.15*EV-detection(EV-Map). A transparent ranking AID, not a validation; the surface/EV terms are PREDICTIONS/DETECTIONS, not measured EV-surface exposure. Recomputable exactly from this DB.

has_activation_state_pdb_pair

1 if a curated ACTIVE/INACTIVE PDB pair exists (only 11 targets).

in_cev_map

Detected in the EV-Map plasma-EV dataset (Rai & Greening 2025, Nat Cell Biol, 10.1038/s41556-025-01795-7) = 3,422 apt-scout targets (broad detected proteome). The EV-Map CONSERVED EV proteome is 182 proteins (42 non-EV); apt-scout matches 104 of these conserved EV-hallmark proteins as targets by gene (the other 78 are not apt-scout targets). Use the ev_hallmark_targets query for that subset. IMPORTANT: EV-Map detection means the protein is EV CARGO (present in the vesicle) — it does NOT mean surface-exposed. Rai & Greening 2025 run a separate membrane-impermeant biotinylation assay giving a 151-protein SURFACEOME, and show the conserved SDCBP/syntenin is luminal (not surface-accessible). For genuine EV-surface accessibility use that 151-protein set, not EV-Map presence.

has_known_aptamer

1 if PubMed '(gene) AND (aptamer OR SELEX)' returned any hit (KEYWORD co-mention, includes false positives — NOT a verified aptamer). For verified aptamers with Kd, see the Binding-affinities (v_kd) layer.

opentargets_top_disease_score

Open Targets association score (0-1).

aptamer_count_pubmed

Number of PubMed hits for (this protein) AND (aptamer OR SELEX). Keyword co-occurrence — verify each (many co-mention without a real aptamer).

aptamer_pmids

The actual PubMed IDs behind the aptamer evidence — click each to read the paper. This is the source of the 'has aptamer' claim.

surface_class

PREDICTED membrane topology (HPA-derived, not a measurement): A_surface = integral/ecto cell-surface (predicted EV-surface accessible); A2_pm_peripheral = plasma-membrane cytoplasmic-leaflet (SRC/LYN/RHOA, predicted not reachable); A_assoc = secreted/corona; B_cargo = luminal cargo; unknown = no HPA localization. Lipid asymmetry can partially flip (PS via scramblase); confirm by protease-protection / intact-EV surface labelling. See v_surface_targets.

116 rows where has_activation_state_pdb_pair = 0, has_known_aptamer = 1 and surface_class = "A2_pm_peripheral" sorted by evidence_priority descending

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CREATE VIEW v_targets AS
SELECT f.id, n.gene_symbol, n.protein_name, tg.tier,
 -- evidence_priority: DETERMINISTIC, reproducible from real DB columns (no LLM).
 -- Transparent weights over harvested evidence: structure 0.35, disease importance
 -- 0.30 (Open Targets top-disease score), PREDICTED surface accessibility 0.20,
 -- EV detection 0.15. A heuristic ranking aid, not a validation; surface/EV terms
 -- are predictions/detections, NOT measured EV-surface exposure.
 ROUND(
   0.35*(CASE WHEN CAST(COALESCE(f.pdb_count_total,'0') AS INTEGER)>0 THEN 1.0
              WHEN CAST(COALESCE(NULLIF(f.alphafold_mean_pLDDT,''),'0') AS REAL)>0 THEN 0.3 ELSE 0.0 END)
 + 0.30*MIN(CAST(COALESCE(NULLIF(f.opentargets_top_disease_score,''),'0') AS REAL), 1.0)
 + 0.20*(CASE sc.surface_class WHEN 'A_surface' THEN 1.0 WHEN 'A_assoc' THEN 0.5 WHEN 'A2_pm_peripheral' THEN 0.2 ELSE 0.0 END)
 + 0.15*(CASE WHEN CAST(COALESCE(f.in_cev_map,0) AS INTEGER)=1 THEN 1.0 ELSE 0.0 END)
 , 3) AS evidence_priority,
 (CASE WHEN CAST(COALESCE(f.pdb_count_total,'0') AS INTEGER)>0 THEN 1 ELSE 0 END) AS has_structure,
 sc.surface_class,
 f.pdb_count_total, f.alphafold_mean_pLDDT, f.has_cryoEM,
 f.has_activation_state_pdb_pair, f.activation_state_pdb_active, f.activation_state_pdb_inactive,
 f.has_known_aptamer, f.aptamer_count_pubmed, ap.aptamer_pmids,
 f.in_cev_map, f.opentargets_top_disease_name, f.opentargets_top_disease_score
FROM v_target_full f
LEFT JOIN target_names n ON n.target_id=f.id
LEFT JOIN targets tg ON tg.id=f.id
LEFT JOIN target_aptamer_pmids ap ON ap.target_id=f.id
LEFT JOIN membrane_surface_class sc ON sc.target_id=f.id;