Evidence claim

Relevance of ProteinGym v1.3 AMFR seeded-random control to "Assess methods for protein stability experiments"

Use case: Assess methods for protein stability experiments
Assessed by: ProteinGym v1.3 AMFR seeded-random control
Relevance: Proxy evidence
Endpoint: One fixed-seed random ranking of the mixed AMFR stability cohort.

A recorded null control helps inspect the assay and evaluation procedure. It is not a biological prediction method recommendation, a chance-performance interval or a matched comparison with the separately executed ESM-2 protocol.

1 reviewed evaluation

Seeded random ranking control on ProteinGym v1.3 AMFR substitution assay

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.

45 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Citation locations 3 values source id rewire-local-20260921-source-proteingym-random locator /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results source id rewire-local-20260921-instructions-proteingym-random locator Pinned reproduction instructions and execution scope source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods (N0); Analysis populations Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id rewire-local-20260921-source-proteingym-random locator /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results source id rewire-local-20260921-instructions-proteingym-random locator Pinned reproduction instructions and execution scope source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods (N0); Analysis populations Context-only references	Seeded random ranking control: report Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id rewire-local-20260921-source-proteingym-random locator /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results source id rewire-local-20260921-instructions-proteingym-random locator Pinned reproduction instructions and execution scope source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods (N0); Analysis populations Context-only references	AMFR matched single-substitution pilot: plan and execution prerequisites Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 194a78b37eed911d0872e9b047a2539a9fee5dd0 Retrieved: 2026-09-25T15:28:11Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `a3208aa4537e8d28c56f68f4559299f31241c50b8d8b2b3776cba5f1718caa43` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values All 2,972 AMFR variants, mixing single and double substitutions; a single fixed seed of 0. SHA256 ranking of prepared variant IDs; no biological prediction or label fitting. Protocol-only mapping; keep its evaluation and configuration separate from ESM-2 and the planned singles comparison. Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values All 2,972 AMFR variants, mixing single and double substitutions; a single fixed seed of 0. SHA256 ranking of prepared variant IDs; no biological prediction or label fitting. Protocol-only mapping; keep its evaluation and configuration separate from ESM-2 and the planned singles comparison. Context-only references	Seeded random ranking control: report Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values All 2,972 AMFR variants, mixing single and double substitutions; a single fixed seed of 0. SHA256 ranking of prepared variant IDs; no biological prediction or label fitting. Protocol-only mapping; keep its evaluation and configuration separate from ESM-2 and the planned singles comparison. Context-only references	AMFR matched single-substitution pilot: plan and execution prerequisites Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 194a78b37eed911d0872e9b047a2539a9fee5dd0 Retrieved: 2026-09-25T15:28:11Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `a3208aa4537e8d28c56f68f4559299f31241c50b8d8b2b3776cba5f1718caa43` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint One fixed-seed random ranking of the mixed AMFR stability cohort. Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint One fixed-seed random ranking of the mixed AMFR stability cohort. Context-only references	Seeded random ranking control: report Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint One fixed-seed random ranking of the mixed AMFR stability cohort. Context-only references	AMFR matched single-substitution pilot: plan and execution prerequisites Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 194a78b37eed911d0872e9b047a2539a9fee5dd0 Retrieved: 2026-09-25T15:28:11Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `a3208aa4537e8d28c56f68f4559299f31241c50b8d8b2b3776cba5f1718caa43` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:rewire-protocol-proteingym-amfr-random-v13 Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

3 source records and release history

Seeded random ranking control: report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
Seeded random ranking control: execution and verification instructions · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
AMFR matched single-substitution pilot: plan and execution prerequisites · Original source · 194a78b37eed911d0872e9b047a2539a9fee5dd0

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: use-case-mapping-protein-stability-amfr-random

field: links:assessed_by:rewire-protocol-proteingym-amfr-random-v13
value: rewire-protocol-proteingym-amfr-random-v13
relevance: proxy
endpoint: One fixed-seed random ranking of the mixed AMFR stability cohort.
rationale: A recorded null control helps inspect the assay and evaluation procedure. It is not a biological prediction method recommendation, a chance-performance interval or a matched comparison with the separately executed ESM-2 protocol.
constraints: All 2,972 AMFR variants, mixing single and double substitutions; a single fixed seed of 0.; SHA256 ranking of prepared variant IDs; no biological prediction or label fitting.; Protocol-only mapping; keep its evaluation and configuration separate from ESM-2 and the planned singles comparison.
limitations: One seed does not estimate chance variability or uncertainty. Do not subtract these separate protocol results to assert an evaluated winner.; Local input hashes do not independently authenticate assay bytes against an upstream published checksum.; This control supplies no pathogenicity or clinical suitability evidence; no human scientific review or independent replication is recorded.
revision: 1
reason: Initial review of the separate fixed-seed random control as limited context.
citation locators: source id: rewire-local-20260921-source-proteingym-random; locator: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; source id: rewire-local-20260921-instructions-proteingym-random; locator: Pinned reproduction instructions and execution scope; source id: use-case-source-amfr-pilot-plan-194a78b; locator: Question; Task and data; Methods (N0); Analysis populations
source locator: rewire-local-20260921-source-proteingym-random: /metrics; /coverage; /model_configuration; /protocol_configuration; /provenance; /protocol_results; rewire-local-20260921-instructions-proteingym-random: Pinned reproduction instructions and execution scope; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods (N0); Analysis populations
review: method: automated-source-review; reviewer: codex; reviewer note: Codex research curation; reviewed at: 2026-09-25T15:28:11Z; note: Reviewed as a separate one-seed control, not clinical evidence or a cross-protocol comparison.
reviewed evaluations: rewire-local-20260921-evaluation-proteingym-random
pins: record id: rewire-local-20260921-audit-source-proteingym-random; fields: status; attributes.artifact_sha256; sha256: 205bbfd49a9a4e2c71c58891cc8812149357384bdd627ab6136d9315f112342b; record id: rewire-local-20260921-evaluation-proteingym-random; fields: status; links; attributes.origin; attributes.comparison; sha256: e76e53a7d07aa1d72be2fc4fd874523a424b8163c60d751d37f210163fa834c6; record id: rewire-local-20260921-instructions-proteingym-random; fields: status; attributes.artifact_sha256; sha256: a9654d0c1ec263b3eb27bad36283fcea24fc528809d0796cd5a4d0b025224d0b; record id: rewire-local-20260921-result-proteingym-random-auc; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 6695fea7fad354a3c643dd3896a85da061c3255721140ff2f1035b2c7756f8a7; record id: rewire-local-20260921-result-proteingym-random-mcc; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 7113181ba25396538b13b420b0139eaa7ba560f26434369978e1e00668b9e0c3; record id: rewire-local-20260921-result-proteingym-random-ndcg; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: e1909142699c54e89a194dbb5e783603a2688dc0a1c963fd87dc26aa1ab2b103; record id: rewire-local-20260921-result-proteingym-random-spearman; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: b35491bd731bd8a6f6b88b4484792862451af078d4082286955bce6d890e3959; record id: rewire-local-20260921-result-proteingym-random-top-recall; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: fbddc27873fc8b8b85009f33c5d20e6f070c8ba4261c6763191eab99050ba4b7; record id: rewire-local-20260921-source-proteingym-random; fields: status; attributes.artifact_sha256; sha256: 2f8461d258b913eec221c0c7288122f9657a1f408555e1b5cec0716df81e109a; record id: rewire-protocol-proteingym-amfr-random-v13; fields: status; name; description; facets; source_ids; links; attributes; sha256: bdc87db74d5a85dc700b5a121bf76faf7ce06e278f29b3e879a7e8450bdb4d95; record id: use-case-protein-stability; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 2dd1d0e139a17e51ae72cc5945196ffbb366fe4daa4c20c4efd950346a30a54f; record id: use-case-source-amfr-pilot-plan-194a78b; fields: status; attributes.artifact_sha256; sha256: 16a98424d9332082177873888d6bfbfd0697fe8dea16c71420c5567258fd32c5

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subject: Assess methods for protein stability experiments

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