Data sources & how to verify any value
Every value is traceable to a public source. Target-layer values are mechanically harvested and the raw upstream record is stored per target (raw_json); Kd-layer values carry the exact source sentence (verbatim_quote) and a PubMed ID.
Target layer (5 evidence layers)
| Layer / field | Source | Verify at |
|---|---|---|
| 1 · Structure (PDB count, resolution, pLDDT, cryo-EM) | RCSB PDB · AlphaFold DB · EMDB | rcsb.org · alphafold.ebi.ac.uk |
| 2 · Modification (PTM counts) | UniProt (modified-residue records) | uniprot.org |
| 2 · Activation-state PDB pairs | Human-curated list of real PDB IDs | rcsb.org (open both structures) |
| 3 · Interaction (drugs, aptamers, antibodies) | Open Targets · ChEMBL · PubMed · Aptagen · HPA | PubMed query + PMIDs in raw_json |
| 4 · Expression / EV-proteome membership | Human Protein Atlas · Vesiclepedia · ExoCarta · EV-Map (Rai 2025) | proteinatlas.org · evmap |
| 5 · Disease (association + score) | Open Targets Platform | platform.opentargets.org |
Binding-affinity (Kd) layer
| Field | Source / meaning | Verify at |
|---|---|---|
| kd_value / kd_unit / kd_log10_molar | Reported dissociation constant, extracted from the source paper | verbatim_quote per row |
| verbatim_quote | The exact sentence / table cell the value came from | shown in each row |
| measurement_class | intrinsic (equilibrium vs purified target) vs non_intrinsic (apparent/cellular or avidity) | assigned per record |
| source_pmid | PubMed ID of the source publication | pubmed.ncbi.nlm.nih.gov |
| tier | Gold = paper-grade, verbatim-verified | — |
One known data note
A raw provenance-citation table contained ~8,669 extraction-bug artefacts (4-letter word fragments mis-captured as PDB IDs); these are excluded from the published v_citations view (valid PDB/PMID/DOI only) while the raw table is retained unmodified for reproducibility. priority_score is a model-assisted heuristic, not an experimental value.
Citations & attribution — please cite the original sources
apt-scout aggregates data from the resources below. If you use apt-scout, please cite the primary sources for the data you rely on, and respect each resource's own licence/terms. apt-scout itself is CC BY 4.0; upstream data remain under their owners' terms.
- RCSB PDB (experimental structures) — Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000;28:235–242. doi:10.1093/nar/28.1.235 · rcsb.org
- AlphaFold (method) — Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583–589. doi:10.1038/s41586-021-03819-2
- AlphaFold DB (predicted models, pLDDT) — Varadi M, Anyango S, Deshpande M, et al. Nucleic Acids Res 2022;50:D439–D444. doi:10.1093/nar/gkab1061 · alphafold.ebi.ac.uk
- EMDB (cryo-EM maps) — wwPDB Consortium / EMDB team. EMDB—the Electron Microscopy Data Bank. Nucleic Acids Res 2024;52:D456–D465. doi:10.1093/nar/gkad1019 · ebi.ac.uk/emdb
- UniProt (sequences, PTM) — The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res 2023;51:D523–D531. doi:10.1093/nar/gkac1052 · uniprot.org
- Human Protein Atlas (tissue expression) — Uhlén M, Fagerberg L, Hallström BM, et al. Tissue-based map of the human proteome. Science 2015;347:1260419. doi:10.1126/science.1260419 · HPA subcellular localization (used for the surface/cargo split): Thul PJ et al. A subcellular map of the human proteome. Science 2017;356:eaal3321. doi:10.1126/science.aal3321 · proteinatlas.org
- Open Targets Platform (disease, drugs) — Ochoa D, Hercules A, Carmona M, et al. The next-generation Open Targets Platform. Nucleic Acids Res 2023;51:D1353–D1359. doi:10.1093/nar/gkac1046 · platform.opentargets.org
- ChEMBL (bioactivities, drugs) — Zdrazil B, Felix E, Hunter F, et al. The ChEMBL Database in 2023. Nucleic Acids Res 2024;52:D1180–D1192. doi:10.1093/nar/gkad1004 · ebi.ac.uk/chembl
- EV-Map (circulating-EV proteome/lipidome) — a resource of the Greening laboratory — Rai A, Claridge B, Lozano J, Greening DW, et al. Nat Cell Biol 2025;27:2167. doi:10.1038/s41556-025-01795-7 · evmap.shinyapps.io/evmap
- Vesiclepedia (EV proteomes) — Chitti SV, Gummadi S, Kang T, et al. (Mathivanan lab). Vesiclepedia 2024. Nucleic Acids Res 2024;52:D1694–D1698. doi:10.1093/nar/gkad1007 · microvesicles.org
- ExoCarta (exosome proteomes) — Keerthikumar S, Chisanga D, Ariyaratne D, et al. ExoCarta: A Web-Based Compendium of Exosomal Cargo. J Mol Biol 2016;428:688–692. doi:10.1016/j.jmb.2015.09.019 · exocarta.org
- PubMed / NCBI Entrez (literature, PMIDs) — Sayers EW et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (annual Database issue). pubmed.ncbi.nlm.nih.gov
- Aptagen Apta-Index (aptamer sequences/evidence) — Aptagen, LLC. aptagen.com/apta-index (commercial resource; cite per its terms)
- Binding-affinity (Kd) layer — verbatim-extracted by the corpus literature-extraction pipeline (E. Doi, NCNP); each record carries its own source PubMed ID and a verbatim quote.
All DOIs above were individually verified against the publisher record (no DOI is shown unless confirmed). Where a resource issues periodic database-update papers, please cite the version matching the data release you used. EV-Map, ExoCarta, Vesiclepedia, ChEMBL, Open Targets, HPA, UniProt, PDB, AlphaFold and EMDB each remain the work of their respective authors and are subject to their own licences/terms.
Human verification worksheet → How to cite apt-scout Download / API