Result

MAE (pairwise, target average as printed, computed per assay and weighted by compound count) of MM/PBSA scoring after a 1 ns simulation on Four-target subset of the public FEP benchmark

N/A MAE (pairwise, target average as printed, computed per assay and weighted by compound count)

Methods

Tested configuration: MM/PBSA scoring after a 1 ns simulation
Protocol: FEP+ benchmark four-target subset, affinity ranking and cost
Dataset: Four-target subset of the public FEP benchmark
Procedure: FEP+ benchmark four-target subset, affinity ranking and cost
Evaluation: MM/PBSA on the FEP+ benchmark four-target subset
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Author-reported evaluation · source checkedBoltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "MM/PBSA", column "PMAE", sub-column "target avg." (text-layer line 1714)

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: Not reported
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 12, row "MM/PBSA", column "PMAE", sub-column "target avg." (text-layer line 1714) 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 author reported 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-t12-mm-pbsa-pmae

metric: mean-absolute-error
metric direction: lower
unit: kilocalorie-per-mole
printed value: N/A
source locator: Table 12, row "MM/PBSA", column "PMAE", sub-column "target avg." (text-layer line 1714)
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: pairwise, target average as printed, computed per assay and weighted by compound count
unit detail: Unit not printed in the table header; appendix D.2.2 states that all predictions are converted to kcal/mol before the metrics are computed
missing metadata: uncertainty: reason: unreported; value: reason: inapplicable; note: Printed as N/A. The source prints no value for this metric on this arm and does not say why; the arm either produces a score rather than an affinity in kcal/mol, or predicts only relative affinities, so the non-centered columns do not apply

Related records

evaluation: MM/PBSA on the FEP+ benchmark four-target subset

Suggest a correction