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Benchmark

Scaffold-Lab unconditional generation

Unified evaluation of protein backbone generation methods: 100 backbones per length group are refolded with ProteinMPNN and ESMFold and scored for designability, novelty, diversity and runtime.

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7 protocols with results

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Methods and evaluation design

Procedure, tasks and evaluated configurations

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Baseline coverage

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Baseline status by linked protocol

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Evidence

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Evidence table

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Release 2026-10-23-5347695500ed · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: lit-structure-20261011-scaffoldlab-benchmark-scaffold-lab

areas
protein-structure
contexts
research
entity level
suite
version
As published 2026
task
Generate protein backbones unconditionally and evaluate them in a shared refolding pipeline
scope note
Per group, 100 backbones with 10 ProteinMPNN sequences each are refolded; a backbone is designable if the refolded structure shares a TM-score above 0.5 with it. Short covers lengths 50 and 100, medium 200 to 500 and long 600 to 1000.
source locator
Table 2 (length grouping), Table 3, and the Metrics section (designability, novelty, diversity, efficiency, ranking)
limitations
Methods are evaluated only at the lengths the authors could run them at, so the groups hold different method sets.
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