Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500) of FrameDiff (Scaffold-Lab unconditional generation) on Scaffold-Lab generated backbones (100 per length group)
0.448 Designability (Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500)
Methods
- Tested configuration
- FrameDiff (Scaffold-Lab unconditional generation)
- Protocol
- Scaffold-Lab unconditional generation: Designability(↑)
- Dataset
- Scaffold-Lab generated backbones (100 per length group)
- Procedure
- Scaffold-Lab unconditional generation: Designability(↑)
- Evaluation
- FrameDiff Designability(↑) on Scaffold-Lab unconditional generation, length 500
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedScaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Designability(↑)'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Medium group, length 500
- Adaptation
- None; methods run with their released weights inside the Scaffold-Lab pipeline
- Scoring implementation
- Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.448 Individual claims | Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Designability(↑)' Version: Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text) | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsExtraction: Parsed the pinned Europe PMC JATS XML with extract_scaffoldlab.py (table-wrap grid with rowspan and colspan expanded, type and method columns forward-filled); row and column labels asserted. Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Designability(↑)' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework · Original source · Version of record, PLoS Computational Biology 2026 (PMC13225634 JATS full text)
Technical metadata and extraction receipts
Stable ID: lit-structure-20261011-scaffoldlab-result-designability-framediff-medium-500
- metric
- designability
- metric direction
- higher
- unit
- fraction
- printed value
- 0.448
- source locator
- Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Designability(↑)'
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Reviewer re-retrieved the Europe PMC JATS XML and matched its SHA-256; an independent table-grid parse matched all 140 per-length cells and all 20 mean Ci and rank records (mean Ci recomputed for all 10 groups); a hand sample of 45 values against the rendered PMC HTML matched.; reviewer: claude; reviewer note: Claude review agent reviewer-ps-2, independent of the extractor lit-protein-structure; no human review claimed; date: 2026-10-11; artifact sha256: 9ff68ef80dc57d6ef85920d4d2104e86d071215ac9c74367a72b2a85669840d0; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13225634/fullTextXML; note: Extraction: Parsed the pinned Europe PMC JATS XML with extract_scaffoldlab.py (table-wrap grid with rowspan and colspan expanded, type and method columns forward-filled); row and column labels asserted. Table 3, row 'Medium' / 'FrameDiff' / length 500, column 'Designability(↑)' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md.
- numeric value
- 0.448
- metric qualifier
- Table 3 'Designability' column, printed as a group mean without data preprocessing; the Metrics section counts a backbone as designable when the mean sc-TM of its top 3 ProteinMPNN sequences refolded with ESMFold exceeds 0.5 (equation 1); the table does not state whether the value is the share of designable backbones or a mean sc-TM; not comparable with the 2 Angstrom sc-RMSD criterion in the concept definition; length 500
- missing metadata
- uncertainty: reason: unreported
- printed value basis
- Value as printed in Table 3
- scope note
- Length group Medium; length 500