Evidence claim

Relevance of ProteinGym v1.3 AMFR substitution assay to "Assess methods for protein stability experiments"

Use case: Assess methods for protein stability experiments
Assessed by: ProteinGym v1.3 AMFR substitution assay
Relevance: Proxy evidence
Endpoint: Ranking the mixed AMFR assay cohort by proteolysis-inferred folding stability using ESM-2 8M masked marginals.

This completed short-construct assay is a narrow example for assessing stability-ranking evidence. Its mixed single/double cohort does not directly answer the planned single-substitution comparison or establish transfer to another protein.

1 reviewed evaluation

ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay

Evidence

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Evidence table

Inspect claims, sources and review details

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60 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 4 values source id rewire-local-20260920-source-proteingym-esm2 locator /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results source id rewire-local-20260920-instructions-proteingym locator Data and method; Reproduce source id profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801 locator AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods; Gates and execution order; Runtime and cost Context-only references	Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-23T18:39:35.604049+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `a8f498011532a74aa9fe556a50555a75e928c5837d19c06a87592ae04049b308` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 4 values source id rewire-local-20260920-source-proteingym-esm2 locator /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results source id rewire-local-20260920-instructions-proteingym locator Data and method; Reproduce source id profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801 locator AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods; Gates and execution order; Runtime and cost Context-only references	ProteinGym v1.3 AMFR substitution assay: reproduction instructions Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `5acb7b2769aae657d48d23c282319e7c69b8ed0424b3c02c875637df7f8dd9fb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 4 values source id rewire-local-20260920-source-proteingym-esm2 locator /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results source id rewire-local-20260920-instructions-proteingym locator Data and method; Reproduce source id profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801 locator AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods; Gates and execution order; Runtime and cost Context-only references	ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `6a14b3866141d5779c76da8071d85c73b7cce0dc4e101c93122706873e847d26` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 4 values source id rewire-local-20260920-source-proteingym-esm2 locator /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results source id rewire-local-20260920-instructions-proteingym locator Data and method; Reproduce source id profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801 locator AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns source id use-case-source-amfr-pilot-plan-194a78b locator Question; Task and data; Methods; Gates and execution order; Runtime and cost Context-only references	AMFR matched single-substitution pilot: plan and execution prerequisites Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost 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 One 47-residue AMFR construct and all 2,972 variants, comprising 820 singles and 2,152 doubles; no train/test split. Exact esm2_t6_8M_UR50D checkpoint, wild-type-context masked marginals summed over substituted sites, CPU, one thread; no assay labels, alignment or structure as scorer inputs. Protocol-only mapping: a direct reviewed task-membership relationship is not recorded. Context-only references	Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-23T18:39:35.604049+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `a8f498011532a74aa9fe556a50555a75e928c5837d19c06a87592ae04049b308` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values One 47-residue AMFR construct and all 2,972 variants, comprising 820 singles and 2,152 doubles; no train/test split. Exact esm2_t6_8M_UR50D checkpoint, wild-type-context masked marginals summed over substituted sites, CPU, one thread; no assay labels, alignment or structure as scorer inputs. Protocol-only mapping: a direct reviewed task-membership relationship is not recorded. Context-only references	ProteinGym v1.3 AMFR substitution assay: reproduction instructions Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `5acb7b2769aae657d48d23c282319e7c69b8ed0424b3c02c875637df7f8dd9fb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values One 47-residue AMFR construct and all 2,972 variants, comprising 820 singles and 2,152 doubles; no train/test split. Exact esm2_t6_8M_UR50D checkpoint, wild-type-context masked marginals summed over substituted sites, CPU, one thread; no assay labels, alignment or structure as scorer inputs. Protocol-only mapping: a direct reviewed task-membership relationship is not recorded. Context-only references	ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `6a14b3866141d5779c76da8071d85c73b7cce0dc4e101c93122706873e847d26` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values One 47-residue AMFR construct and all 2,972 variants, comprising 820 singles and 2,152 doubles; no train/test split. Exact esm2_t6_8M_UR50D checkpoint, wild-type-context masked marginals summed over substituted sites, CPU, one thread; no assay labels, alignment or structure as scorer inputs. Protocol-only mapping: a direct reviewed task-membership relationship is not recorded. Context-only references	AMFR matched single-substitution pilot: plan and execution prerequisites Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost 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 Ranking the mixed AMFR assay cohort by proteolysis-inferred folding stability using ESM-2 8M masked marginals. Context-only references	Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-23T18:39:35.604049+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `a8f498011532a74aa9fe556a50555a75e928c5837d19c06a87592ae04049b308` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Ranking the mixed AMFR assay cohort by proteolysis-inferred folding stability using ESM-2 8M masked marginals. Context-only references	ProteinGym v1.3 AMFR substitution assay: reproduction instructions Original source ↗ rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `5acb7b2769aae657d48d23c282319e7c69b8ed0424b3c02c875637df7f8dd9fb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

4 source records and release history

ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
ProteinGym v1.3 AMFR substitution assay: reproduction instructions · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2
Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
AMFR matched single-substitution pilot: plan and execution prerequisites · Original source · 194a78b37eed911d0872e9b047a2539a9fee5dd0

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-protein-stability-amfr-esm2

field: links:assessed_by:rewire-protocol-proteingym-amfr-v13
value: rewire-protocol-proteingym-amfr-v13
relevance: proxy
endpoint: Ranking the mixed AMFR assay cohort by proteolysis-inferred folding stability using ESM-2 8M masked marginals.
rationale: This completed short-construct assay is a narrow example for assessing stability-ranking evidence. Its mixed single/double cohort does not directly answer the planned single-substitution comparison or establish transfer to another protein.
constraints: One 47-residue AMFR construct and all 2,972 variants, comprising 820 singles and 2,152 doubles; no train/test split.; Exact esm2_t6_8M_UR50D checkpoint, wild-type-context masked marginals summed over substituted sites, CPU, one thread; no assay labels, alignment or structure as scorer inputs.; Protocol-only mapping: a direct reviewed task-membership relationship is not recorded.
limitations: No interval or seed-variability estimate; training overlap remains unknown and assay bytes have not been independently authenticated against an upstream checksum.; Recorded inference timing excludes loading, preparation and metrics; peak memory is unreported.; The site-independent and full EVmutation methods in the planned singles study have no completed comparison here.; No general whole-protein, ProteinGym-wide or clinical inference; automated source review is not human scientific validation.
revision: 1
reason: Initial bounded applicability review of the existing AMFR ESM-2 evaluation.
citation locators: source id: rewire-local-20260920-source-proteingym-esm2; locator: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; source id: rewire-local-20260920-instructions-proteingym; locator: Data and method; Reproduce; source id: profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801; locator: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; source id: use-case-source-amfr-pilot-plan-194a78b; locator: Question; Task and data; Methods; Gates and execution order; Runtime and cost
source locator: rewire-local-20260920-source-proteingym-esm2: /metrics; /coverage; /execution/adapter_provenance; /execution; /input_information; /provenance; /protocol_results; rewire-local-20260920-instructions-proteingym: Data and method; Reproduce; profile-protocol-proteingym-reference-files-dms-substitutions-csv-a8f49801: AMFR_HUMAN_Tsuboyama_2023_4G3O row: seq_len, selection_assay, raw_DMS_phenotype_name and mutant-count columns; use-case-source-amfr-pilot-plan-194a78b: Question; Task and data; Methods; Gates and execution order; Runtime and cost
review: method: automated-source-review; reviewer: codex; reviewer note: Codex research curation; reviewed at: 2026-09-25T15:28:11Z; note: Reviewed existing measured evidence separately from the planned singles comparison. No new experiment, human domain review or clinical validation.
reviewed evaluations: rewire-local-20260920-evaluation-proteingym-esm2
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subject: Assess methods for protein stability experiments

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