scout: v_kd: 6 rows where assay_method = "BLI", sequence_status = "verified_in_text_or_SI" and tier = "Gold" sorted by kd_log10

742 distinct verbatim-verified aptamer–target Kd measurements (canonical Gold v1; 555 intrinsic-equilibrium; 300 unique targets; 287 publications; 435 carry a verbatim-verified sequence). ★HOW TO READ: 'kd_reported' is the value EXACTLY as written in the paper (units are MIXED — pM/nM/M — so it is NOT directly comparable). To compare, sort, or train an ML model, use ONLY 'kd_log10_molar' (lower = tighter) and filter measurement_class=intrinsic + target_type=protein. The same target appears in several rows because of different aptamers, assays, conditions (temperature/buffer) or papers — see those columns. For a clean ready-to-use subset use the 'kd_ready_to_use' query. Source: corpus literature-extraction pipeline (E. Dohi).

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

target_name_canonical: Target as named in the source paper.
target_type: protein / cell-line+EV / glycan-conjugate. Filter to 'protein' for molecular targets.
target_uniprot: UniProt accession when a human protein (sparse for now; links to apt-scout target).
aptamer_name: Aptamer identifier as reported.
kd_reported: Kd value AS REPORTED in the paper (value + unit). Units are MIXED — do NOT compare this column directly.
kd_log10_molar: log10(Kd in molar). THE column to sort / compare / learn on (lower = tighter).
measurement_class: intrinsic = equilibrium vs purified target; non_intrinsic = apparent/cellular or avidity (NOT comparable to intrinsic).
binding_constant_type: Kd / apparent-Kd etc. as reported.
assay_method: SPR / filter binding / flow cytometry / ITC / BLI …
assay_temperature_k: Assay temperature (K) — a reason the same pair can have several rows.
source_pmid: PubMed ID of the source paper (links out).
verbatim_quote: The exact sentence the value was taken from.
verification_level: QC status (honest, growing): human_verified / human_corrected = a logged human verdict from the stratified-random sample; multi_agent_verified = passed independent multi-agent (L2) check; extraction_verified = extraction-pipeline verified; automated. Human verification is in progress: as of this release 0 records carry a logged human verdict — the published set is multi-agent-/extraction-verified, and human spot-checking is being added post-publication (version-tracked). No record is labelled human_verified without a logged human review.
sequence_status: Aptamer-sequence provenance: verified_in_text_or_SI = sequence verbatim-verified against the source text/SI (shown); pending_manual_supp / pending_supp_oa / pending_manual_figure = sequence reported only in a (often paywalled) SI or a figure, being curated post-submission; no_single_sequence_pool = a pool/library/primer, no single sequence exists.
pi_provenance_flag: PI manual-review flag: KEEP_seq_in_figure = valid record, sequence is in a 3D-structure figure; FLAG_cited_data = Kd may be a value cited from elsewhere, re-verify. (EXCLUDE rows are hidden from this view.)
seq_source: original (already in source DB) / backfill_text_verified (recovered from paper or SI text).

6 rows where assay_method = "BLI", sequence_status = "verified_in_text_or_SI" and tier = "Gold" sorted by kd_log10_molar

descending

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id	target_name_canonical	target_type	target_uniprot	aptamer_name	aptamer_seq	kd_reported	kd_log10_molar ▼	measurement_class	binding_constant_type	tier	source_origin	verification_level	sequence_status	seq_source	assay_method	assay_temperature_k	assay_ph	assay_buffer	aptamer_chemistry	aptamer_modifications	source_pmid	doi	verbatim_quote	source_db
421	hnRNP A1	protein	P09651	AS1411	GGTGGTGGTGGTTGTGGTGGTGGTGG	1.75e-08 M	-7.757	intrinsic	Kd	Gold	v4	multi_agent_verified	verified_in_text_or_SI	original	BLI		7.4	BLI buffer (20 mM phosphate buffer, 8 mM KCl, 137 mM NaCl, 0.05% surfactant P20)	DNA		38784467	10.1039/d3md00752a	for AS1411, the K d value was 17.5 nM (Fig. 6B)	step2c_acs_v1
422	hnRNP A1	protein	P09651	TBA	GGTTGGTGTGGTTGG	2.1100000000000004e-08 M	-7.676	intrinsic	Kd	Gold	v4	multi_agent_verified	verified_in_text_or_SI	original	BLI		7.4	BLI buffer (20 mM phosphate buffer, 8 mM KCl, 137 mM NaCl, 0.05% surfactant P20)	DNA		38784467	10.1039/d3md00752a	for TBA, the K d value was 21.1 nM (Fig. 6A)	step2c_acs_v1
373	beta-conglutin	protein		11-mer	GGTGGGGGTGG	2.3300000000000003e-08 M	-7.633	intrinsic	Kd	Gold	v4	multi_agent_verified	verified_in_text_or_SI	original	BLI	303.15	7.4	PBS, 1.5 mM MgCl2, pH 7.4, 0.1% Tween-20	DNA		33498970	10.3390/ijms22031150	A 2:1 heterogenous model was used to fit the data and calculate the binding affinities resulting in two different KD values of 6.95 and 23.30 nM.	step2c_acs_v1
253	rmCD3 d ε	protein		CD3_Apt1 dimer	CCCGATTGATTCGCAATGTGCGTCCCCTCGTGCC	25.2 nM	-7.599	non_intrinsic	Kd	Gold	v4	extraction_verified	verified_in_text_or_SI	backfill_text_verified	BLI	298.15		PBS +/+ buffer	2'F-RNA	dimerized via ssDNA scaffold	38745854	10.1016/j.omtn.2024.102198	The affinity of the dimeric aptamer was determined by OCTET and was 25.2 nM for Apt1 dimer	step2c_literal_v3
98	thrombin	protein	P00734	HD22 (TA-TT)	AGTCCGTGGTAGGGCAGGTTGGGGTGACTGTAAACGCTCGCTTCGATCTAGTCCGTGGGGGCAGGGGGGTGACTAGCAGATATGCATCCGTAGC	27.8 nM	-7.556	intrinsic	Kd	Gold	v4	extraction_verified	verified_in_text_or_SI	original	BLI			buffer used for the bead-based selection, which contains Tween-20	DNA	Biotin (5' end)	37531184	10.1021/acschembio.3c00183	TA - TT \| 27.80 ± 0.09	step2c_literal_v3
254	rmCD3 d ε	protein		CD3_Apt12 dimer	TCCCCTGTCGATATCCACCGTCTGGCCCGCATTGA	218.0 nM	-6.662	non_intrinsic	Kd	Gold	v4	extraction_verified	verified_in_text_or_SI	backfill_text_verified	BLI	298.15		PBS +/+ buffer	2'F-RNA	dimerized via ssDNA scaffold	38745854	10.1016/j.omtn.2024.102198	218 nM for Apt12 dimer	step2c_literal_v3

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CREATE VIEW v_kd AS
SELECT k.id,
 target_name_canonical,
 CASE
   WHEN target_name_canonical LIKE '%cell%' OR target_name_canonical LIKE '%vesicle%' OR target_name_canonical LIKE '%exosome%' THEN 'cell/EV'
   WHEN target_name_canonical LIKE '%BSA%' OR target_name_canonical LIKE '%sLe%' OR target_name_canonical LIKE '%glycan%' OR target_name_canonical LIKE '% Le %' THEN 'glycan/conjugate'
   ELSE 'protein'
 END AS target_type,
 target_uniprot, aptamer_name, aptamer_seq,
 (COALESCE(kd_value,'') || CASE WHEN COALESCE(kd_unit,'')!='' THEN ' '||kd_unit ELSE '' END) AS kd_reported,
 CAST(NULLIF(kd_log10_molar,'') AS REAL) AS kd_log10_molar,
 measurement_class, binding_constant_type, 'Gold' AS tier, k.tier AS source_origin,
 CASE
   WHEN vh.verdict='confirmed' THEN 'human_verified'
   WHEN vh.verdict='corrected' THEN 'human_corrected'
   WHEN vh.verdict='rejected'  THEN 'human_rejected'
   WHEN k.verification_status='agent_verified_L2' THEN 'multi_agent_verified'
   WHEN k.verification_status IN ('verified','CONFIRM') THEN 'extraction_verified'
   ELSE 'automated'
 END AS verification_level,
 sequence_status, seq_source, pi_provenance_flag,
 assay_method,
 CAST(NULLIF(assay_temperature_k,'') AS REAL) AS assay_temperature_k,
 CAST(NULLIF(assay_ph,'') AS REAL) AS assay_ph,
 assay_buffer, assay_cations, aptamer_chemistry, aptamer_modifications,
 source_pmid, doi, verbatim_quote, source_db
FROM kd_measurements k LEFT JOIN verification_human vh ON vh.row_id=k.source_record_id
WHERE LOWER(COALESCE(k.include_in_gold,''))='true';

Binding affinities (Kd) — source-verified (view)

6 rows where assay_method = "BLI", sequence_status = "verified_in_text_or_SI" and tier = "Gold" sorted by kd_log10_molar

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