Configuration

AF3 (pTM) as a screening score

Ranks a compound library by predicted template modeling score, estimating global structural accuracy taken from the predicted protein-ligand complex.

1 evaluation · 10 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

1 evaluation · 10 results. Different protocols are not a single leaderboard.

Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) · Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025

Sorted by AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets)	AUROC (AUROC, median over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets)	Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets)	Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets)
AF3 (pTM) as a screening scoreEvaluation	0.832	0.874	0.417	0.396	13.7	13.3	12.6	11.9	9.34	9.5

All 10 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.832 AUROC (AUROC, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'AUROC' (Mean)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.874 AUROC (AUROC, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'AUROC' (Med)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.417 Bedroc (BEDROC with alpha = 80.5, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'BEDROC (α = 80.5)' (Mean)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	0.396 Bedroc (BEDROC with alpha = 80.5, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'BEDROC (α = 80.5)' (Med)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	13.7 Enrichment factor (EF at the top 0.5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF0.5%' (Mean)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	13.3 Enrichment factor (EF at the top 0.5% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF0.5%' (Med)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	12.6 Enrichment factor (EF at the top 1% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF1%' (Mean)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	11.9 Enrichment factor (EF at the top 1% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF1%' (Med)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	9.34 Enrichment factor (EF at the top 5% of the ranked library, mean over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF5%' (Mean)
Configuration: AF3 (pTM) as a screening score	Protocol: DEKOIS 2.0 screening with co-folding confidence scores against docking tools (Shen et al. 2025 Table 1) Dataset: DEKOIS 2.0, 79 targets as scored by Shen et al. 2025	9.5 Enrichment factor (EF at the top 5% of the ranked library, median over the 79 DEKOIS 2.0 targets) unitless · higher Uncertainty: Not reported by the source: The source prints no interval or spread for this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1) hitdisc-20261022-protocol-shen-dekois-builtin Aggregation: Not reported Shen et al. 2025, Chemical Science (Europe PMC full text) · Table 1, row 'AF3 (pTM)', column 'EF5%' (Med)

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-config-af3-ptm

areas: molecular-interactions
contexts: research
method types: foundation_model
reported name: AF3 (pTM)
configuration type: paper_evaluation
foundation model eligible: true
review: method: scope-review; automated-source-review; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Read the record against the pinned sources and against docs/use-cases.md and docs/record-contract.md.; note: Record checked against the pinned source and the record contract. Transcription checked; not reproduced and not reviewed by a human scientist.; artifact sha256: 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12704515/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
version: AlphaFold3 version 3.0.0, five predictions with random seed 1, Jackhmmer MSAs (HMMER 3.4.0)
access reuse: Source code at https://github.com/google-deepmind/alphafold3, https://github.com/bytedance/Protenix and https://github.com/jwohlwend/boltz (Data availability); no licence is stated in the source
parameters: All parameters other than the sample count and seed left at default or recommended values
score training overlap: Not assessed for this score by the source beyond the ligand-similarity analysis of Figure 5 and Fig. S10
source locator: Methods 'Complex structure prediction' and 'Scoring schemes'

Related records

configuration of: AlphaFold 3
system: AF3 (pTM) on DEKOIS 2.0 (Shen et al. 2025 Table 1)

Suggest a correction