track · audited-with-caveats · verified 2026-07-21
ProteinGym DMS Indels
ProteinGym track for predicting experimental fitness measurements of insertion and deletion mutants across deep-mutational-scanning assays.
Audited with caveats: 2 field(s) are marked provisional or conflicted. Warnings are shown next to affected values and these claims are excluded from unqualified comparisons.
Benchmark definition
What is counted
- Version
- 1.3
- Total
- 66Conflicted · medium (DMS assays)
- Task formats
- zero-shot mutation-effect prediction; supervised mutation-effect prediction
- Capabilities
- Modalities
Version history
| Version | Status | Release / as-of | Total | Formal tracks |
|---|---|---|---|---|
1.0proteingym-dms-indel-v10 | superseded | 2023-12-08 | 66 (DMS assays) | None registered |
1.3proteingym-dms-indel-v13 | current | 2025-04-27 | 66Conflicted · medium (DMS assays) | None registered |
Tracks and subsets
| ID | Count | Basis | Partition? | Notes |
|---|---|---|---|---|
Binding function categorybinding-function-assays | 0 | assays | No | Neither Table A2 nor the v1.3 coarse_selection_type field contains an indel Binding assay. |
Scientific Task Atlas
Scientific task classification
complete for 1.3. Formal DMS indel track; source conflicts on assay count remain flagged on the benchmark.
| Scientific task | Coverage | Count | Mapping | Evidence |
|---|---|---|---|---|
| Protein mutation-effect prediction | explicitly-in-scope | 66 assays DMS assays. | official-track high confidence | proteingym-dms-indel-evidence-v13The underlying benchmark field carries the audit caveat. |
| Protein fitness prediction | explicitly-in-scope | 66 assays DMS assays. | official-track high confidence | proteingym-dms-indel-evidence-v13Overlapping claim; not an additive task total. |
Scientific coverage notes
| Domain | Coverage | Count | Interpretation |
|---|---|---|---|
| Protein design | explicitly-in-scope | Not reported | The track uses fitness-prediction and design-oriented metrics, but design is not a separately counted subset. |
| Protein-protein binding | not-in-scope | 0 | The official generic Binding function category contains zero indel assays in the paper and current reference file. |
| Protein-ligand binding | not-in-scope | 0 | The official generic Binding function category contains zero indel assays in the paper and current reference file. |
Evaluation registry
Works and run settings
A setting change—scope, prompt, tools, budget, grader, or repeats—creates a separate run. Charts never cross a comparability group.
No normalized evaluation run is published yet. Creator evidence is still attached below.
Evidence and change history
Source locators remain visible; expand an item to inspect the exact Registry fields it supports.
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · section: pp. 1–10, Figure 1 and Sections 3–5 (Track definition, parent relationship, domains, modalities, formats, capabilities, and access.) · Supports 10 fields
/name/organizations/release_date/latest_version/kind/summary/domains/capabilities/modalities/task_formats
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · table: pp. 6, 29–30; Tables 1, A1, and A2 (66 v1.0 indel assays and zero Binding indel assays.) · Supports 3 fields
/versions/0/task_counts/total/versions/0/task_counts/basis/versions/0/task_counts/subsets
proteingym-dms-indel-v13-resource · repository-path: DMS_indels.csv and DMS_ProteinGym_indels.zip in Zenodo record 15293562 (Both expose 66 assay records; no coarse_selection_type=Binding row.) · Supports 8 fields
/task_counts/total/task_counts/basis/task_counts/subsets/versions/1/task_counts/total/versions/1/task_counts/basis/versions/1/task_counts/subsets/scientific_task_classification/entries/0/scientific_task_classification/entries/1
proteingym-dms-indel-repository-resource · repository-path: README.md Overview at tag PG_v1.3 (States 74 DMS indel assays.) · Supports 2 fields
/task_counts/total/versions/1/task_counts/total
proteingym-dms-indel-repository-resource · repository-path: README.md Resources, Results, Usage and reproducibility, Releases, and License (Current version, downloads, public scoring, implementation pin, and MIT license.) · Supports 9 fields
/latest_version/access/level/access/tasks/access/artifacts/access/grader/access/license/access/biosafety_notes/resources/implementations
Unresolved field claims
/task_counts/totalConflicted · medium — The v1.3 archive/reference file contains 66 assays while the official PG_v1.3 README states 74.
Evidence: proteingym-dms-indel-evidence-v13, proteingym-dms-indel-evidence-readme/versions/1/task_counts/totalConflicted · medium — The v1.3 archive/reference file contains 66 assays while the official PG_v1.3 README states 74.
Evidence: proteingym-dms-indel-evidence-v13, proteingym-dms-indel-evidence-readme