ProtGPT2
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence.
Overview
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence.
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: ProtGPT2 | Task: PFMBench ANTI-RES: Antibiotic resistance Dataset subset: Antibiotic resistance (PFMBench split) | 0.684 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Anti.Res.) |
| Configuration: ProtGPT2 | Task: PFMBench BINDING-DB: BindingDB Dataset subset: BindingDB (PFMBench split) | 0.172 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Bind. DB) |
| Configuration: ProtGPT2 | Task: PFMBench CLONING-CLF: Cloning CLF Dataset subset: Cloning CLF (PFMBench split) | 0.777 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Clo. CLF) |
| Configuration: ProtGPT2 | Task: PFMBench DEEPLOC2: DeepLoc2 Multi Dataset subset: DeepLoc2 Multi (PFMBench split) | 0.703 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(DL2 M.) |
| Configuration: ProtGPT2 | Task: PFMBench DEEPSOL: DeepSol Dataset subset: DeepSol (PFMBench split) | 0.789 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(DeepSol) |
| Configuration: ProtGPT2 | Task: PFMBench EC: Enzyme Commission Dataset subset: Enzyme Commission (PFMBench split) | 0.697 f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(EC) |
| Configuration: ProtGPT2 | Task: PFMBench MAT-PROD: Material production Dataset subset: Material production (PFMBench split) | 0.768 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Mat.Pro.) |
| Configuration: ProtGPT2 | Task: PFMBench METAL-ION: Metal ion binding Dataset subset: Metal ion binding (PFMBench split) | 0.712 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(M. I. Bin.) |
| Configuration: ProtGPT2 | Task: PFMBench PDB-BIND: PDBbind Dataset subset: PDBbind (PFMBench split) | 0.135 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(PDBBind) |
| Configuration: ProtGPT2 | Task: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Dataset subset: ProteinGym (PFMBench split) | 0.19 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(ProteinGym) |
| Configuration: ProtGPT2 | Task: PFMBench SEC-STRUCT: Secondary structure Dataset subset: Secondary structure (PFMBench split) | 0.494 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Sec. Str.) |
| Configuration: ProtGPT2 | Task: PFMBench STABILITY: TAPE_Stability Dataset subset: TAPE_Stability (PFMBench split) | 0.148 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtGPT2 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(ProtGPT2 [ 12 ]), column(Stability) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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Evidence
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Evidence table
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Sources and history
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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-protgpt2
- areas
- proteins-complexes
- source locator
- Table 3, row(ProtGPT2 [ 12 ])
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: ProtGPT2 on PFMBench ANTI-RES: Antibiotic resistance
- model: ProtGPT2 on PFMBench BINDING-DB: BindingDB
- model: ProtGPT2 on PFMBench CLONING-CLF: Cloning CLF
- model: ProtGPT2 on PFMBench DEEPLOC2: DeepLoc2 Multi
- model: ProtGPT2 on PFMBench DEEPSOL: DeepSol
- model: ProtGPT2 on PFMBench EC: Enzyme Commission
- model: ProtGPT2 on PFMBench MAT-PROD: Material production
- model: ProtGPT2 on PFMBench METAL-ION: Metal ion binding
- model: ProtGPT2 on PFMBench PDB-BIND: PDBbind
- model: ProtGPT2 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- model: ProtGPT2 on PFMBench SEC-STRUCT: Secondary structure
- model: ProtGPT2 on PFMBench STABILITY: TAPE_Stability