Result

Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) of OpenFE under a fixed automated protocol on OpenFE subset of the public FEP benchmark

N/A Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count)

Methods

Tested configuration: OpenFE under a fixed automated protocol
Protocol: FEP+ benchmark OpenFE subset, affinity ranking
Dataset: OpenFE subset of the public FEP benchmark
Procedure: FEP+ benchmark OpenFE subset, affinity ranking
Evaluation: OpenFE on the FEP+ benchmark OpenFE subset
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Evaluation origin not reported · source checkedBoltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "OpenFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1694)

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Held-out affinity test set
Adaptation: Fixed automated protocol with no per-system adjustment
Scoring implementation: Appendix D.2.2 'Evaluation metrics': Pearson R, Kendall tau, pairwise MAE (PMAE), MAE and the fraction of predictions within 1 and 2 kcal/mol, each computed per assay and averaged across assays weighted by compound count, with predictions converted to kcal/mol first; the centered variants translate each assay's predictions to the ground-truth mean

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row 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
Reported result N/A Individual claims	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Table 11, row "OpenFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1694) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	source checked ["source-hash-verification","pdf-text-parse","independent-cell-check","rendered-source-visual-check","ai-assisted-source-review"] · 2026-10-22T13:40:00Z unreported Audit details Independent review 2026-10-22: the printed value was re-read from the pinned artifact with a parser written for this review and matches, together with the numeric value, metric concept, qualifier, direction, unit, uncertainty, locator and the configuration, protocol and dataset the result hangs off. Cells the source prints as N/A or '-' carry no numeric value and a recorded reason. Field: `attributes.printed_value` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf Inspected artifact Extraction artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` Extraction artifact

How to read the evidence

Sources and history

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

1 source record and release history

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Original source · bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-result-t11-openfe-within-2-non-centered

metric: proportion
metric direction: higher
unit: fraction
printed value: N/A
source locator: Table 11, row "OpenFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1694)
review: method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; ai-assisted-source-review; method note: Re-retrieved all three sources and matched each pinned SHA-256. Re-rendered the Boltz-2 supplement with pdftotext -layout (poppler 26.08.0) and matched the text layer's recorded SHA-256. Re-read all 256 cells with a parser written for this review that does not import the extraction script, matching each result to its cell through its own source_locator, and separately read appendix tables 11, 12 and 14 from PNG renderings of PDF pages 29 and 30 at 160 dpi, and Ross Table 3 from the pinned XML markup. Checked printed value, numeric value, locator, metric concept, qualifier, direction, unit, uncertainty and the linked configuration, protocol and dataset, and that every N/A or '-' cell is recorded as missing with a reason.; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; reviewed at: 2026-10-22T13:40:00Z; artifact sha256: be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/supplementaryFiles; note: Independent review 2026-10-22: the printed value was re-read from the pinned artifact with a parser written for this review and matches, together with the numeric value, metric concept, qualifier, direction, unit, uncertainty, locator and the configuration, protocol and dataset the result hangs off. Cells the source prints as N/A or '-' carry no numeric value and a recorded reason.
numeric value: Not reported
metric qualifier: within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count
unit detail: Counted entity: predictions. The header reads 'Perc.' but appendix D.2.2 defines the column as the fraction of predictions with absolute error below the threshold, and the printed values lie on a 0 to 1 scale
missing metadata: uncertainty: reason: unreported; value: reason: inapplicable; note: Printed as N/A. The source does not label the cell, but appendix D.2.2 bears on it: the centered variants exist because they allow "a fair comparison with methods that only predict relative affinities, such as relative FEP", and this arm is relative FEP, which fixes no absolute scale for a non-centered error to measure. The ABFE arm, which computes absolute free energies, prints values in both columns on the same table.

Related records

evaluation: OpenFE on the FEP+ benchmark OpenFE subset

Suggest a correction