Site-Independent
Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
2 evaluations · 19 results. Different protocols are not a single leaderboard.
Sorted by Spearman (higher 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 | Protocol and dataset | Spearman | Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays)) | Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman) | Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Site-Independent [ProteinGym 144fe22b snapshot]Evaluation | ProteinGym AMFR official zero-shot Spearman snapshot, ProteinGym AMFR 4G3O official snapshot cohort | 0.358 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| Site-Independent [ProteinGym 144fe22b snapshot]Evaluation | ProteinGym v1.3 zero-shot DMS substitutions, ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Not reported | 0.369 | 0.344 | 0.343 | 0.317 | 0.38 | 0.427 | 0.359 | 0.376 | 0.383 | 0.389 | 0.318 | 0.358 | 0.337 | 0.24 | 0.241 | 0.273 | 0.35 | 0.375 |
All 19 result rows with coverage, uncertainty and sources
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym AMFR official zero-shot Spearman snapshot Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort | 0.358 Spearman unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent AMFR official snapshot Not reported Aggregation: Not reported ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=Site-Independent |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.359 Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays)) unitless · higher Uncertainty: SE 0.012. From compute_bootstrap_standard_error_functional_categories in performance_DMS_benchmarks.py at 144fe22 (default 10,000 resamples, lines 95-111 and 310-315); not an absolute standard error of the model's own average. Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Average_Spearman' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.337 Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Depth_1' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.24 Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Depth_2' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.241 Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Depth_3' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.273 Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Depth_4' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.35 Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Depth_5+' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.369 Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Function_Activity' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.344 Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Function_Binding' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.343 Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Function_Expression' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.383 Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Function_OrganismalFitness' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.358 Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Function_Stability' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.317 Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'High_MSA_depth' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.427 Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Low_MSA_depth' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.376 Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Medium_MSA_depth' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.38 Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Taxa_Human' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.389 Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Taxa_Other_Eukaryote' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.318 Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Taxa_Prokaryote' |
| Configuration: Site-Independent [ProteinGym 144fe22b snapshot] | Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | 0.375 Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceSite-Independent: ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 77, row 'Site-Independent', column 'Taxa_Virus' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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How it works, versions and access
Versions and evaluated configurations
- Site-Independent [ProteinGym 144fe22b snapshot] · configuration of
Strengths, limitations and unresolved questions
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds. Individual claims | Protocol metadata evidence: proteingym-paper.xml profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10723403 retrieved 2026-09-23 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-fbaafadc4cef4f56932a Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds. Individual claims | Abstract: Mutation effects predicted from sequence co-variation profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-fbaafadc4cef4f56932a Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. |
| Description Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds. Individual claims | ProteinGym AMFR assay-level Spearman comparison profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-fbaafadc4cef4f56932a Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- ProteinGym AMFR assay-level Spearman comparison · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
- Abstract: Mutation effects predicted from sequence co-variation · Original source · Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017
- Protocol metadata evidence: proteingym-paper.xml · Original source · PMC10723403 retrieved 2026-09-23
Technical metadata and extraction receipts
Stable ID: uc20260930-method-site-independent
- areas
- proteins-complexes
- source locator
- Pinned ProteinGym Spearman CSV header: Site-Independent
- review
- method: automated-source-review; reviewer: codex; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.; reviewer note: role: experimental use-case curation
- entity level
- method
- identity scope
- Family/method identity only; no undocumented checkpoint equivalence.
Related records
- subject: Site-Independent: description
- configuration of: Site-Independent [ProteinGym 144fe22b snapshot]