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Benchmark

Public binding free energy benchmark (Ross et al. 2023)

Assembled collection of proteins and congeneric small-molecule series with measured affinities, used to score relative binding free energy predictions against experiment.

Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.

4 protocols with results

Overview

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

Results on linked records

This benchmark has no results of its own in this release. 4 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 8 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

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Evidence table

Inspect claims, sources and review details

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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
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How to read the evidence

Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-benchmark-fep-public

areas
molecular-interactions
contexts
research
entity level
suite
version
As curated for Ross et al. 2023; data released as the public_binding_free_energy_benchmark repository, releases v1.0 and v2.0 (both 2023-06-26, MIT)
task
Relative binding affinity prediction for congeneric series
scope note
Table 3 (FEP+ accuracy beside experimental reproducibility), Table 2 (the data sets and their compound counts) and Table 1 (the assay-reproducibility survey) extracted. Per-system values in the Supplementary Results and the repository were not retrieved. The Boltz-2 supplement's two subsets of this collection are recorded as separate protocols.
source locator
Ross et al. 2023 Tables 1-3; Boltz-2 supplement appendix D.2.1 and E.2.1
limitations
Ross et al. 2023 states its results use release v1.0 of the public benchmark repository; the Boltz-2 supplement does not state which release its subsets come from.; The 876-complex OpenFE subset and the 87-compound 4-target subset both derive from this collection and must partly overlap, so results on the two subsets are not independent. Neither source states the overlap.
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: f371d2e373306588d11b695b8de21b253a90293d6a15884f635bcf927bdebb1d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10576784/fullTextXML
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