Evidence claim

Relevance of CASP16 affinity challenge, target-averaged to ranking analogues of a hit

Use case: Rank close analogues of a hit by binding affinity
Assessed by: CASP16 affinity challenge, Boltz-2 against the top-ranked participants
Relevance: Proxy evidence
Endpoint: Target-average Pearson R, Kendall tau and absolute error of predicted against withheld measured affinities on the CASP16 chymase and autotaxin ligand sets

Judgement of how closely this protocol answers the lead-optimisation ranking decision. Drafted by the extracting agent; not reviewed.

10 reviewed evaluations

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.

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19 evidence rows 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
Citation locations 1 values source id uc-leadopt-20261022-source-boltz2-supplement locator Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` 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
Comparison group blind-casp16 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` 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
Comparison title Blind affinity ranking in CASP16 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` 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
Constraints 3 values Keep the Boltz-2 row, which its developers report, distinct from the participant rows, which the supplement compiles. Do not read a per-target value from this table; the same two series are recorded per-target for PLABench and those values are not these values. Do not treat the anonymous group identifiers as named methods. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` 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
Endpoint Target-average Pearson R, Kendall tau and absolute error of predicted against withheld measured affinities on the CASP16 chymase and autotaxin ligand sets Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` 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
Claimed field links:assessed_by:uc-leadopt-20261022-protocol-boltz2-casp16 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` 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
Headline metric kendall-tau Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` 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
Limitations 5 values Reported by the developers of the machine-learning model being promoted, and the participants' submissions were not obtained independently. The mmseqs 90% identity filtering applied to the other affinity benchmarks was not applied here; the stated protection is that the data was released after the training cutoff and that maximum compound Tanimoto similarity to the training set was 0.41 and 0.59. No per-series value and no uncertainty are printed. The supplement says nothing about what methods the participant groups used. The chymase series spans a narrow affinity range, which the CASP16 assessors say limits how well the challenge resolves accuracy. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` 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
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Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` 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
Rationale This is blind evidence on two pharmaceutical ligand sets whose affinities were withheld until after submission, which is the closest thing in this batch to a prospective read, and its aggregation is the same within-target-then-averaged form as the FEP+ benchmark protocols. It is proxy rather than direct evidence for a different reason: neither source establishes that the chymase and autotaxin ligand sets are congeneric series around one confirmed hit, so this measures ranking inside a target's ligand set rather than ranking a hit's close analogues. The CASP16 assessors describe the two sets by their affinity range and count, not by a shared scaffold. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` 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

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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-judgement-boltz2-casp16

field: links:assessed_by:uc-leadopt-20261022-protocol-boltz2-casp16
value: uc-leadopt-20261022-protocol-boltz2-casp16
relevance: proxy
endpoint: Target-average Pearson R, Kendall tau and absolute error of predicted against withheld measured affinities on the CASP16 chymase and autotaxin ligand sets
rationale: This is blind evidence on two pharmaceutical ligand sets whose affinities were withheld until after submission, which is the closest thing in this batch to a prospective read, and its aggregation is the same within-target-then-averaged form as the FEP+ benchmark protocols. It is proxy rather than direct evidence for a different reason: neither source establishes that the chymase and autotaxin ligand sets are congeneric series around one confirmed hit, so this measures ranking inside a target's ligand set rather than ranking a hit's close analogues. The CASP16 assessors describe the two sets by their affinity range and count, not by a shared scaffold.
constraints: Keep the Boltz-2 row, which its developers report, distinct from the participant rows, which the supplement compiles.; Do not read a per-target value from this table; the same two series are recorded per-target for PLABench and those values are not these values.; Do not treat the anonymous group identifiers as named methods.
limitations: Reported by the developers of the machine-learning model being promoted, and the participants' submissions were not obtained independently.; The mmseqs 90% identity filtering applied to the other affinity benchmarks was not applied here; the stated protection is that the data was released after the training cutoff and that maximum compound Tanimoto similarity to the training set was 0.41 and 0.59.; No per-series value and no uncertainty are printed.; The supplement says nothing about what methods the participant groups used.; The chymase series spans a narrow affinity range, which the CASP16 assessors say limits how well the challenge resolves accuracy.
comparison group: blind-casp16
comparison title: Blind affinity ranking in CASP16
stratum label: CASP16 affinity challenge, target-averaged
stratum order: 1
headline metric: kendall-tau
citation locators: source id: uc-leadopt-20261022-source-boltz2-supplement; locator: Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14
source locator: Appendix D.2.1 'Data leakage control'; D.2.2 'Evaluation metrics' and 'Baselines'; Tables 11, 12 and 14
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 quoted wording was matched against the pinned artifact and the locator checked.
reviewed evaluations: uc-leadopt-20261022-eval-t14-bacpi; uc-leadopt-20261022-eval-t14-boltz-2; uc-leadopt-20261022-eval-t14-boltz-2-iptm; uc-leadopt-20261022-eval-t14-gat; uc-leadopt-20261022-eval-t14-lg008; uc-leadopt-20261022-eval-t14-lg016; uc-leadopt-20261022-eval-t14-lg055; uc-leadopt-20261022-eval-t14-lg082; uc-leadopt-20261022-eval-t14-lg204; uc-leadopt-20261022-eval-t14-lg207
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fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 5e53a63e32cdbe0599acb7fb822f2bb0f0f006d9fd5ca314950c756e2476d968; record id: uc-leadopt-20261022-result-t14-lg207-pmae; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: f2b84e56b51751671b7ab4a7d9a2fc67c3b50eacc1bae24f308355b7f7ac26a2; record id: uc-leadopt-20261022-result-t14-lg207-within-1-centered; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: aefee2cc9ae77970d4d8ed01e4f89b16f37ba1990bdf123e4588a5d1c69a0d8b; record id: uc-leadopt-20261022-result-t14-lg207-within-1-non-centered; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: f06845d2a0e0dee7b285d6c39fcb27438b41915e9d5689ffb968b41643e12dea; record id: uc-leadopt-20261022-result-t14-lg207-within-2-centered; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 66b1171a679cd4583e9330e438682df97b99dfe7f10aa856b6dd8d095b8bfc45; record id: uc-leadopt-20261022-result-t14-lg207-within-2-non-centered; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: aee2190cf457e8ff68ffb851b709e56cca64a9c2558eb596c2bb460902b39f6c; record id: uc-leadopt-20261022-source-boltz2-supplement; fields: status; attributes.artifact_sha256; sha256: 6e31fabd2a46f1b867adbf58be440609b0060aca9e10abcfe9723259cef3bb46; record id: use-case-lead-optimisation-affinity-ranking; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 7432deaf6a9ac54d76ccc53abb33ca8b040bf88886f79afd081a08dd686511df
reason: First evidence for this use case: the blind CASP16 read on two withheld ligand sets, independently reviewed against its pinned artifact on 2026-10-22.

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subject: Rank close analogues of a hit by binding affinity

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