Abstract: Mutation effects predicted from sequence co-variation
Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 · Peer-reviewed
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Claims
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- Baseline: Predict missense variant effects in a protein of interest: Baseline Site-independent alignment model (run-doc-proteingym-readme-md-144fe22b: README lines 66-70)
- EVmutation: description: Description Unsupervised statistical model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects while explicitly capturing dependencies between residue positions. (qa-descriptions-20261011-a-source-hopf2017: abstractText ('EVmutation, an unsupervised statistical method for predicting the effects of mutations that explicitly captures residue dependencies between positions'); profile-protocol-proteingym-paper-xml-a58110e0: Baselines (alignment-based models 'are trained on Multiple Sequence Alignments'))
- Site-Independent: description: 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. (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'))
Models, benchmarks and other records
Methods (2)
Evidence
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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.
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27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 6a91a29373ab03b0ebd3a03a7655536bd6abec369d1385146b4f94d1e0b5fbec Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1038%2Fnbt.3769%22&format=json&resultType=core Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Doi 10.1038/nbt.3769 Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| 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 metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Media type application/json Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Missing metadata: licence: note Europe PMC record gives no licence Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Missing metadata: licence: reason unreported Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Publication status peer_reviewed Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Retrieved at 2026-10-11T00:38:38Z Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
| Review: date 2026-10-11 Source metadata | Abstract: Mutation effects predicted from sequence co-variation No field-specific location recorded Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 | catalogued 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. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Source text retrieved and hashed for the issue #88 placeholder-description fix.
Technical metadata and extraction receipts
Stable ID: qa-descriptions-20261011-a-source-hopf2017
- url
- https://doi.org/10.1038/nbt.3769
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1038%2Fnbt.3769%22&format=json&resultType=core
- version
- Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017
- retrieved at
- 2026-10-11T00:38:38Z
- artifact sha256
- 6a91a29373ab03b0ebd3a03a7655536bd6abec369d1385146b4f94d1e0b5fbec
- publication status
- peer_reviewed
- media type
- application/json
- source locator
- abstractText
- doi
- 10.1038/nbt.3769
- 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.
- missing metadata
- licence: reason: unreported; note: Europe PMC record gives no licence
- review
- method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. 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.; receipt: data/omics/qa-descriptions-20261011-a/review.json; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1038%2Fnbt.3769%22&format=json&resultType=core