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Boltz-2 affinity prediction

Boltz-2 run as published to co-fold the complex from sequence and ligand and read a binding affinity in kcal/mol off its affinity head.

3 evaluations · 28 results

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Evaluations and results

3 evaluations · 28 results. Different protocols are not a single leaderboard.

Sorted by Kendall tau (target average as printed, computed per assay and weighted by compound count) (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	Protocol and dataset	Kendall tau (target average as printed, computed per assay and weighted by compound count)	MAE (centered, computed per assay and averaged across assays weighted by compound count)	MAE (non-centered, computed per assay and averaged across assays weighted by compound count)	MAE (pairwise, target average as printed, computed per assay and weighted by compound count)	Pearson (target average as printed, computed per assay and weighted by compound count)	Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count)	Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count)	Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count)	Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count)	Accelerator time (per-method cost as printed beside the accuracy columns)
Boltz-2 affinity predictionEvaluation	FEP+ benchmark four-target subset, affinity ranking and cost, Four-target subset of the public FEP benchmark	0.48 (best in column)	0.59 (best in column)	0.75 (best in column)	0.85 (best in column)	0.66 (best in column)	0.83 (best in column)	0.69 (best in column)	0.98 (best in column)	0.97 (best in column)	20 GPU sec
Boltz-2 affinity predictionEvaluation	FEP+ benchmark OpenFE subset, affinity ranking, OpenFE subset of the public FEP benchmark	0.46	0.64	1.22	0.93	0.62	0.8	0.49	0.96	0.82	Not reported
Boltz-2 affinity predictionEvaluation	CASP16 affinity challenge, Boltz-2 against the top-ranked participants, CASP16 affinity targets L1000 and L3000	0.45	0.95	1.28	1.36	0.65	0.61	0.48	0.9	0.81	Not reported

All 28 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.46 Kendall tau (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Kendall tau", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.64 MAE (centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "MAE", sub-column "cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	1.22 MAE (non-centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "MAE", sub-column "non-cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.62 Pearson (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Pearson R", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.93 MAE (pairwise, target average as printed, computed per assay and weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "PMAE", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.8 Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Perc. within 1", sub-column "cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.49 Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Perc. within 1", sub-column "non-cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.96 Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Perc. within 2", sub-column "cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.82 Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2", column "Perc. within 2", sub-column "non-cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.48 Kendall tau (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Kendall tau", sub-column "target avg." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.59 MAE (centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "MAE", sub-column "cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.75 MAE (non-centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "MAE", sub-column "non-cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.66 Pearson (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Pearson R", sub-column "target avg." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.85 MAE (pairwise, target average as printed, computed per assay and weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "PMAE", sub-column "target avg." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	20 GPU sec Accelerator time (per-method cost as printed beside the accuracy columns) second · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "time" (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.83 Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Perc. within 1", sub-column "cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.69 Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Perc. within 1", sub-column "non-cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.98 Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Perc. within 2", sub-column "cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.97 Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2", column "Perc. within 2", sub-column "non-cent." (text-layer line 1706)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	0.45 Kendall tau (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "Kendall tau", sub-column "target avg." (text-layer line 1747)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	0.95 MAE (centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "MAE", sub-column "cent." (text-layer line 1747)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	1.28 MAE (non-centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "MAE", sub-column "non-cent." (text-layer line 1747)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	0.65 Pearson (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "Pearson R", sub-column "target avg." (text-layer line 1747)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	1.36 MAE (pairwise, target average as printed, computed per assay and weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "Pairwise MAE", sub-column "target avg." (text-layer line 1747)
Configuration: Boltz-2 affinity prediction	Protocol: CASP16 affinity challenge, Boltz-2 against the top-ranked participants Dataset: CASP16 affinity targets L1000 and L3000	0.61 Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Boltz-2 on the CASP16 affinity challenge uc-leadopt-20261022-protocol-boltz2-casp16 Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 14, row "Boltz-2", column "Perc. within 1", sub-column "cent." (text-layer line 1747)

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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)

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Stable ID: uc-leadopt-20261022-config-boltz2-affinity

areas: molecular-interactions
contexts: research
method types: foundation_model
configuration type: paper_evaluation
reported name: Boltz-2
version: Boltz-2 as described in the 2025-06-18 preprint; no checkpoint identifier printed
access reuse: MIT code and weights.
foundation model eligible: true
source locator: Tables 11, 12 and 14, row 'Boltz-2'; appendix D.2.2
missing metadata: checkpoint: reason: unreported; note: The supplement does not name a checkpoint for the affinity benchmarks
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

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configuration of: Boltz-2
system: Boltz-2 on the FEP+ benchmark OpenFE subset
system: Boltz-2 on the FEP+ benchmark four-target subset
system: Boltz-2 on the CASP16 affinity challenge

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