Baseline: Predict missense variant effects in a protein of interest
Baseline of Predict missense variant effects in a protein of interest
Site-independent alignment model
Baseline method for the use case, drafted by the extraction agent; not reviewed.
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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field baseline Context-only references | Abstract: Mutation effects predicted from sequence co-variation run-doc-proteingym-readme-md-144fe22b: README lines 66-70 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Claimed field baseline Context-only references | OATML-Markslab/ProteinGym / README.md run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids1 values
| Abstract: Mutation effects predicted from sequence co-variation run-doc-proteingym-readme-md-144fe22b: README lines 66-70 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
Method ids1 values
| OATML-Markslab/ProteinGym / README.md run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records3 values
| Abstract: Mutation effects predicted from sequence co-variation run-doc-proteingym-readme-md-144fe22b: README lines 66-70 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
Pinned records3 values
| OATML-Markslab/ProteinGym / README.md run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale An alignment-based model that scores each position separately, without the dependencies between positions that EVmutation adds, and with no neural network. It is the first and simplest model in the ProteinGym substitution baselines table (input modality MSA; Hopf et al. 2017). Context-only references | Abstract: Mutation effects predicted from sequence co-variation run-doc-proteingym-readme-md-144fe22b: README lines 66-70 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Rationale An alignment-based model that scores each position separately, without the dependencies between positions that EVmutation adds, and with no neural network. It is the first and simplest model in the ProteinGym substitution baselines table (input modality MSA; Hopf et al. 2017). Context-only references | OATML-Markslab/ProteinGym / README.md run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Context-only references | Abstract: Mutation effects predicted from sequence co-variation run-doc-proteingym-readme-md-144fe22b: README lines 66-70 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Source location run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Context-only references | OATML-Markslab/ProteinGym / README.md run-doc-proteingym-readme-md-144fe22b: README lines 66-70 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c | not individually reviewed No individual claim review recorded Audit detailsField: 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
2 source records and release history
- OATML-Markslab/ProteinGym / README.md · Original source · Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c
- Abstract: Mutation effects predicted from sequence co-variation · Original source · Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017
Technical metadata and extraction receipts
Stable ID: use-case-baseline-protein-variant-effect-prediction
- field
- baseline
- value
- Site-independent alignment model
- method ids
- uc20260930-method-site-independent
- rationale
- An alignment-based model that scores each position separately, without the dependencies between positions that EVmutation adds, and with no neural network. It is the first and simplest model in the ProteinGym substitution baselines table (input modality MSA; Hopf et al. 2017).
- source locator
- run-doc-proteingym-readme-md-144fe22b: README lines 66-70
- review
- reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T16:00:00Z; method: ai-assisted-source-review; scope-review; method note: Checked the method record, the rationale and the cited source lines.; note: Baseline claim checked against docs/use-cases.md (best established pre-machine-learning method).
- pins
- record id: qa-descriptions-20261011-a-source-hopf2017; fields: status; attributes.artifact_sha256; sha256: d81e2685043658ce9a505400aa8ddd58f01e4b91a16f3489293141033fc51188; record id: run-doc-proteingym-readme-md-144fe22b; fields: status; attributes.artifact_sha256; sha256: 70823ddfc9ef5ced58ba8aea340a8d99cf7808ee58b0d2cd4ee1abe5f6684646; record id: use-case-protein-variant-effect-prediction; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 69bd4cb85c9365c7382c7d3f67c197bf2968688d9a83a8012e8763157de61701