Configuration

MM/PBSA scoring after a 1 ns simulation

Thermalises the modelled complex with a restrained minimisation and equilibration, runs 1 ns of unrestrained NPT dynamics and scores the final frame with MM/PBSA.

1 evaluation · 10 results

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Evaluations and results

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

Protocol: FEP+ benchmark four-target subset, affinity ranking and cost · Dataset: Four-target subset of the public FEP benchmark

Sorted by CPU time (per-method cost as printed beside the accuracy columns) (lower 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	CPU time (per-method cost as printed beside the accuracy columns)	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)
MM/PBSA scoring after a 1 ns simulationEvaluation	10-15 CPU min	0.16	N/A	N/A	N/A	0.18	N/A	N/A	N/A	N/A

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Tested configuration	Protocol and dataset	Finding	Evidence and details
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	0.16 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 MM/PBSA 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 "MM/PBSA", column "Kendall tau", sub-column "target avg." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "MAE", sub-column "cent." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "MAE", sub-column "non-cent." (text-layer line 1714)
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	0.18 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 MM/PBSA 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 "MM/PBSA", column "Pearson R", sub-column "target avg." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "PMAE", sub-column "target avg." (text-layer line 1714)
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	10-15 CPU min CPU time (per-method cost as printed beside the accuracy columns) minute · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MM/PBSA 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 "MM/PBSA", column "time" (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "Perc. within 1", sub-column "cent." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "Perc. within 1", sub-column "non-cent." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "Perc. within 2", sub-column "cent." (text-layer line 1714)
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	N/A 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 MM/PBSA 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 "MM/PBSA", column "Perc. within 2", sub-column "non-cent." (text-layer line 1714)

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

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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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Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-config-mmpbsa

areas: molecular-interactions
contexts: research
method types: conventional_pipeline
configuration type: reported_configuration
reported name: MM/PBSA
version: Not printed; the AMBER implementation
source locator: Table 12, row 'MM/PBSA'; appendix D.2.2
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

Related records

configuration of: MM/PBSA (AMBER)
system: MM/PBSA on the FEP+ benchmark four-target subset

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