ProTrek
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence-Structure-Function.
Overview
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence-Structure-Function.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
12 evaluations · 12 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ProTrek | Task: PFMBench ANTI-RES: Antibiotic resistance Dataset subset: Antibiotic resistance (PFMBench split) | 0.593 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench ANTI-RES: Antibiotic resistance Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Anti.Res.) |
| Configuration: ProTrek | Task: PFMBench BINDING-DB: BindingDB Dataset subset: BindingDB (PFMBench split) | 0.192 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench BINDING-DB: BindingDB Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Bind. DB) |
| Configuration: ProTrek | Task: PFMBench CLONING-CLF: Cloning CLF Dataset subset: Cloning CLF (PFMBench split) | 0.826 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench CLONING-CLF: Cloning CLF Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Clo. CLF) |
| Configuration: ProTrek | Task: PFMBench DEEPLOC2: DeepLoc2 Multi Dataset subset: DeepLoc2 Multi (PFMBench split) | 0.839 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench DEEPLOC2: DeepLoc2 Multi Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(DL2 M.) |
| Configuration: ProTrek | Task: PFMBench DEEPSOL: DeepSol Dataset subset: DeepSol (PFMBench split) | 0.834 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench DEEPSOL: DeepSol Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(DeepSol) |
| Configuration: ProTrek | Task: PFMBench EC: Enzyme Commission Dataset subset: Enzyme Commission (PFMBench split) | 0 .76408 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench EC: Enzyme Commission Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(EC) |
| Configuration: ProTrek | Task: PFMBench MAT-PROD: Material production Dataset subset: Material production (PFMBench split) | 0.815 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench MAT-PROD: Material production Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Mat.Pro.) |
| Configuration: ProTrek | Task: PFMBench METAL-ION: Metal ion binding Dataset subset: Metal ion binding (PFMBench split) | 0.804 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench METAL-ION: Metal ion binding Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(M. I. Bin.) |
| Configuration: ProTrek | Task: PFMBench PDB-BIND: PDBbind Dataset subset: PDBbind (PFMBench split) | 0.173 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench PDB-BIND: PDBbind Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(PDBBind) |
| Configuration: ProTrek | Task: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Dataset subset: ProteinGym (PFMBench split) | 0.359 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4. Aggregation: Not reported pfmbench primary benchmark evidence · Table 4, row(ProTrek [ 56 ]), column(ProteinGym) |
| Configuration: ProTrek | Task: PFMBench SEC-STRUCT: Secondary structure Dataset subset: Secondary structure (PFMBench split) | 0.774 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench SEC-STRUCT: Secondary structure Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Sec. Str.) |
| Configuration: ProTrek | Task: PFMBench STABILITY: TAPE_Stability Dataset subset: TAPE_Stability (PFMBench split) | 0.0492 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProTrek on PFMBench STABILITY: TAPE_Stability Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Aggregation: Not reported pfmbench primary benchmark evidence · Table 3, row(ProTrek [ 56 ]), column(Stability) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
Strengths, limitations and unresolved questions
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.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- pfmbench primary benchmark evidence · Original source · 2506.14796v1
Technical metadata and extraction receipts
Stable ID: pfmbench-method-protrek
- areas
- proteins-complexes
- source locator
- Table 3, row(ProTrek [ 56 ])
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: ProTrek on PFMBench ANTI-RES: Antibiotic resistance
- model: ProTrek on PFMBench BINDING-DB: BindingDB
- model: ProTrek on PFMBench CLONING-CLF: Cloning CLF
- model: ProTrek on PFMBench DEEPLOC2: DeepLoc2 Multi
- model: ProTrek on PFMBench DEEPSOL: DeepSol
- model: ProTrek on PFMBench EC: Enzyme Commission
- model: ProTrek on PFMBench MAT-PROD: Material production
- model: ProTrek on PFMBench METAL-ION: Metal ion binding
- model: ProTrek on PFMBench PDB-BIND: PDBbind
- model: ProTrek on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- model: ProTrek on PFMBench SEC-STRUCT: Secondary structure
- model: ProTrek on PFMBench STABILITY: TAPE_Stability