ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
De novo backbones based sequence design, length 100 scTM. Scored with scTM on CASP, CAMEO and de novo backbones. Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs.
Overview
De novo backbones based sequence design, length 100 scTM. Scored with scTM on CASP, CAMEO and de novo backbones. Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- ESM3 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- LM-Design on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- ProteinMPNN on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
sctm (score) · Higher values are better for this metric.
Every method ProteinBench reports on De novo backbones based sequence design, length 100 scTM, scored with scTM on CASP, CAMEO and de novo backbones.
Evaluation protocol · CASP, CAMEO and de novo backbones (ProteinBench split)
- ProteinMPNN · Configuration · Author-reported evaluation0.962
- ESM-IF1 · Configuration · Author-reported evaluation0.810
- LM-Design · Configuration · Author-reported evaluation0.834
- ESM3 · Configuration · Author-reported evaluation0.942
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
proteinbench primary benchmark evidence · Table 2, column(De novo backbones based sequence design, length 100 scTM ↑)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ProteinMPNN · Configuration | 0.962 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 2, row(ProteinMPNN), column(De novo backbones based sequence design, length 100 scTM ↑) |
| ESM-IF1 · Configuration | 0.810 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 100 scTM ↑) |
| LM-Design · Configuration | 0.834 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 2, row(LM-Design), column(De novo backbones based sequence design, length 100 scTM ↑) |
| ESM3 · Configuration | 0.942 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 2, row(ESM3), column(De novo backbones based sequence design, length 100 scTM ↑) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- Many of these metrics are better when lower, including scRMSD, perplexity and binding energy. The direction comes from the arrow in the paper's own header.
- Rows such as Native PDBs and RAbD are the natural reference the authors include for scale, not a competing method.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 4 evaluations · 4 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Configuration: ESM-IF1Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTMDataset subset: CASP, CAMEO and de novo backbones (ProteinBench split) Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.810 sctm Unit: score · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 100 scTM ↑) Source checking is not independent reproduction. |
| ESM3 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Configuration: ESM3Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTMDataset subset: CASP, CAMEO and de novo backbones (ProteinBench split) Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.942 sctm Unit: score · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 2, row(ESM3), column(De novo backbones based sequence design, length 100 scTM ↑) Source checking is not independent reproduction. |
| LM-Design on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Configuration: LM-DesignTask: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTMDataset subset: CASP, CAMEO and de novo backbones (ProteinBench split) Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.834 sctm Unit: score · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 2, row(LM-Design), column(De novo backbones based sequence design, length 100 scTM ↑) Source checking is not independent reproduction. |
| ProteinMPNN on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Configuration: ProteinMPNNTask: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTMDataset subset: CASP, CAMEO and de novo backbones (ProteinBench split) Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.962 sctm Unit: score · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 2, row(ProteinMPNN), column(De novo backbones based sequence design, length 100 scTM ↑) Source checking is not 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 |
|---|---|---|
| Relationship: part of discovery-benchmark-proteinbench Individual claims | proteinbench primary benchmark evidence Table 2, column(De novo backbones based sequence design, length 100 scTM ↑) Version: 2409.06744v1 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: proteinbench-association-if-de-novo-backbones-based-sequence-design-length-100-sctm Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- proteinbench primary benchmark evidence · Original source · 2409.06744v1
Technical metadata and extraction receipts
Stable ID: proteinbench-task-if-de-novo-backbones-based-sequence-design-length-100-sctm
- areas
- proteins-complexes
- tasks
- De novo backbones based sequence design, length 100 scTM
- metric
- scTM
- metric direction
- higher
- dataset
- CASP, CAMEO and de novo backbones
- protocol
- Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs.
- source locator
- Table 2, column(De novo backbones based sequence design, length 100 scTM ↑)
- comparison panels
- id: proteinbench-panel-if-de-novo-backbones-based-sequence-design-length-100-sctm; title: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM; protocol id: proteinbench-task-if-de-novo-backbones-based-sequence-design-length-100-sctm; dataset id: proteinbench-dataset-casp-cameo-and-de-novo-backbones; metric: sctm; unit: score; direction: higher; result ids: proteinbench-result-proteinmpnn-if-de-novo-backbones-based-sequence-design-length-100-sctm-sctm; proteinbench-result-esm-if1-if-de-novo-backbones-based-sequence-design-length-100-sctm-sctm; proteinbench-result-lm-design-if-de-novo-backbones-based-sequence-design-length-100-sctm-sctm; proteinbench-result-esm3-if-de-novo-backbones-based-sequence-design-length-100-sctm-sctm; source ids: expansion-p3-proteinbench; source locator: Table 2, column(De novo backbones based sequence design, length 100 scTM ↑); context: Every method ProteinBench reports on De novo backbones based sequence design, length 100 scTM, scored with scTM on CASP, CAMEO and de novo backbones.; caveats: Author-reported numbers, source checked but not independently reproduced.; Many of these metrics are better when lower, including scRMSD, perplexity and binding energy. The direction comes from the arrow in the paper's own header.; Rows such as Native PDBs and RAbD are the natural reference the authors include for scale, not a competing method.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: ProteinBench
- subject: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: part of discovery-benchmark-proteinbench
- benchmark: ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- benchmark: ESM3 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- benchmark: LM-Design on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM
- benchmark: ProteinMPNN on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM