Evidence claim

Relevance of hitdisc-20261022-protocol-shen-speed to use-case-hit-discovery-virtual-screening

Use case: Find hits for a target by virtual screening
Assessed by: Co-folding time per compound on five DEKOIS 2.0 targets (Shen et al. 2025 Table 5)
Relevance: Proxy evidence
Endpoint: Average wall-clock seconds per compound to co-fold a protein-ligand pair, per target and averaged over five targets

Relevance judgement drafted by the extraction agent. Not reviewed.

6 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.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

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 hitdisc-20261022-source-shen2025 locator See the protocol record's source_locator Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Comparison group co-folding-screening-cost Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Comparison title Compute cost per compound of co-folding Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Compare rows only within this protocol. Enrichment factors from different protocols are not comparable, because the actives-to-inactives ratio and the construction of the negatives differ. Do not read a result from this protocol together with the Mac1 pose results or the CASF-2016 scoring, ranking and docking protocols already in this store: those measure pose and scoring accuracy, not the ranking of a library. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Endpoint Average wall-clock seconds per compound to co-fold a protein-ligand pair, per target and averaged over five targets Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Claimed field links:assessed_by:hitdisc-20261022-protocol-shen-speed Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Headline metric runtime Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Limitations 5 values MSA construction is excluded: pre-computed MSAs were fed as input, so these are inference times only. No docking tool was timed, so the table does not compare co-folding cost with docking cost. Single measurements on five targets with no repeats or uncertainty; the authors note that runtime varies substantially with token length and other factors. Transcribed from the source; no reproduction by Rewire and no human scientific review. No ligand-similarity or pharmacophore baseline is scored on any protocol in this batch, although issue #177 asks for one as the pre-machine-learning comparator alongside docking. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Pinned records 45 values record id hitdisc-20261022-eval-speed-speed-af3-1 fields status links attributes.origin attributes.comparison sha256 b2335eef86a48afbe3f5f3be1b41b44c71b71f46efb9f687896738d25a37881f record id hitdisc-20261022-eval-speed-speed-af3-5 fields status links attributes.origin attributes.comparison sha256 5088dcb168410ee4b15aacfc81ead31031e62bb94fc57fdc02590a1107ce7b54 record id hitdisc-20261022-eval-speed-speed-boltz2-default fields status links attributes.origin attributes.comparison sha256 3c2a0071d7bdfc680df5da9f43947e21fb7a6391ff2975ab6e2e4d1c01c42b85 record id hitdisc-20261022-eval-speed-speed-boltz2-no-affinity fields status links attributes.origin attributes.comparison sha256 819417e70cc5f76464a9a47d8d44da891f701891e1dab2018c33afc1f8b85041 record id hitdisc-20261022-eval-speed-speed-protenix-1 fields status links attributes.origin attributes.comparison sha256 3713dec2def24773c4e2fa873dc166b76daf035ec35fbb4466a071b57c90bdac record id hitdisc-20261022-eval-speed-speed-protenix-5 fields status links attributes.origin attributes.comparison sha256 75d8b75182a436753678c753a50f5c0466797c48ceeccaf06f75eeecacfa2b6a record id hitdisc-20261022-protocol-shen-speed fields status name description facets source_ids links attributes sha256 b272a6a8eb45a75bc2428715fa7a6cbfb89447d483de4d6da79be9e4d324e1aa record id hitdisc-20261022-result-speed-speed-af3-1-a2a fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 6cef3f51d035dbbe9afd2c69c73865309719660a816ecce42c3224cc821895bc record id hitdisc-20261022-result-speed-speed-af3-1-ar fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 0d7e9093be14b06fba18e4a8c3e052fb630daeb8540f06a4bb7841c7ddcf1cc7 record id hitdisc-20261022-result-speed-speed-af3-1-average fields status attributes.metric attributes.metric_qualifier attributes.printed_value 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788db4424ff8a5a02d9b48f67ebffaed41d634c47356cac9b4fddfd488d5d2f8 record id hitdisc-20261022-result-speed-speed-protenix-5-hdac2 fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 80e1e4a8fc8985abf5fa201b05ffa29703f30b84c086c5cd5a58a22be94ef5bd record id hitdisc-20261022-source-shen2025 fields status attributes.artifact_sha256 sha256 f94ba0aaa2aea1b6a65dae4fbc3549071ccac4eeba75390ada5a10f6b5ccd823 record id use-case-hit-discovery-virtual-screening fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 dc57177bbc7bd26bcb01b194ecc3598e987ff5dc02a07432c4585abfde8e97cc Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record
Rationale Proxy: it measures cost rather than ranking, but issue #177 lists compute per compound as a limit to record for every result because it decides whether a method can be run on a library at all. At 7.79 to 34.58 seconds per compound on one H100, a million-compound library would take between about 90 and 400 GPU-days. That multiplication is this agent's arithmetic on the printed per-compound times, not a figure the source prints, and it is the constraint behind the authors' own decision to screen only five of the 15 LIT-PCBA targets. Context-only references	Shen et al. 2025, Chemical Science (Europe PMC full text) Original source ↗ hitdisc-20261022-protocol-shen-speed: see its source_locator Version: PMC12704515 (Chem Sci, published 2025-12-11) Retrieved: 2026-10-22T11:52:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8` Hash scope: Hash scope not separately documented; inspect source record

How to read the evidence

Sources and history

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

1 source record and release history

Shen et al. 2025, Chemical Science (Europe PMC full text) · Original source · PMC12704515 (Chem Sci, published 2025-12-11)

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Technical metadata and extraction receipts

Stable ID: hitdisc-20261022-use-case-mapping-shen-speed

field: links:assessed_by:hitdisc-20261022-protocol-shen-speed
value: hitdisc-20261022-protocol-shen-speed
relevance: proxy
endpoint: Average wall-clock seconds per compound to co-fold a protein-ligand pair, per target and averaged over five targets
rationale: Proxy: it measures cost rather than ranking, but issue #177 lists compute per compound as a limit to record for every result because it decides whether a method can be run on a library at all. At 7.79 to 34.58 seconds per compound on one H100, a million-compound library would take between about 90 and 400 GPU-days. That multiplication is this agent's arithmetic on the printed per-compound times, not a figure the source prints, and it is the constraint behind the authors' own decision to screen only five of the 15 LIT-PCBA targets.
constraints: Inspect every linked evaluation's source locator before citing a result.; Compare rows only within this protocol. Enrichment factors from different protocols are not comparable, because the actives-to-inactives ratio and the construction of the negatives differ.; Do not read a result from this protocol together with the Mac1 pose results or the CASF-2016 scoring, ranking and docking protocols already in this store: those measure pose and scoring accuracy, not the ranking of a library.
limitations: MSA construction is excluded: pre-computed MSAs were fed as input, so these are inference times only.; No docking tool was timed, so the table does not compare co-folding cost with docking cost.; Single measurements on five targets with no repeats or uncertainty; the authors note that runtime varies substantially with token length and other factors.; Transcribed from the source; no reproduction by Rewire and no human scientific review.; No ligand-similarity or pharmacophore baseline is scored on any protocol in this batch, although issue #177 asks for one as the pre-machine-learning comparator alongside docking.
citation locators: source id: hitdisc-20261022-source-shen2025; locator: See the protocol record's source_locator
source locator: hitdisc-20261022-protocol-shen-speed: see its source_locator
headline metric: runtime
comparison group: co-folding-screening-cost
comparison title: Compute cost per compound of co-folding
stratum label: Five DEKOIS 2.0 targets, one NVIDIA H100
stratum order: 1
reason: Hit-discovery use-case pass 2026-10-22: relevance of a protocol to a new use case (rewire-benchmark-data #177).
review: method: scope-review; automated-source-review; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; date: 2026-10-22; method note: Read the record against the pinned sources and against docs/use-cases.md and docs/record-contract.md.; note: Claim checked against the pinned source. Every figure it states was matched to a result record in this batch.; artifact sha256: 11a4cee97057d9e72f9393024d22fdd169e3134f493367eee2f7869facf9ccf8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12704515/fullTextXML; receipt: data/omics/use-case-coverage-hitdisc-20261022/review.json
reviewed evaluations: hitdisc-20261022-eval-speed-speed-af3-1; hitdisc-20261022-eval-speed-speed-af3-5; hitdisc-20261022-eval-speed-speed-boltz2-default; hitdisc-20261022-eval-speed-speed-boltz2-no-affinity; hitdisc-20261022-eval-speed-speed-protenix-1; hitdisc-20261022-eval-speed-speed-protenix-5
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