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ProstT5

ProstT5: Protein foundation model.

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Evaluations and results

11 evaluations · 11 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Accuracy	Spearman	AUROC	F1 max (multi-label; TorchDrug-style F1_score_max)
ProstT5Evaluation	PFMBench MAT-PROD: Material production, Material production (PFMBench split)	0 .81622 (best in column)	Not reported	Not reported	Not reported
ProstT5Evaluation	PFMBench SEC-STRUCT: Secondary structure, Secondary structure (PFMBench split)	0 .81397	Not reported	Not reported	Not reported
ProstT5Evaluation	PFMBench METAL-ION: Metal ion binding, Metal ion binding (PFMBench split)	0.721	Not reported	Not reported	Not reported
ProstT5Evaluation	PFMBench ANTI-RES: Antibiotic resistance, Antibiotic resistance (PFMBench split)	0.69	Not reported	Not reported	Not reported
ProstT5Evaluation	PFMBench BINDING-DB: BindingDB, BindingDB (PFMBench split)	Not reported	0.166	Not reported	Not reported
ProstT5Evaluation	PFMBench CLONING-CLF: Cloning CLF, Cloning CLF (PFMBench split)	Not reported	Not reported	0.799	Not reported
ProstT5Evaluation	PFMBench DEEPLOC2: DeepLoc2 Multi, DeepLoc2 Multi (PFMBench split)	Not reported	Not reported	Not reported	0.732
ProstT5Evaluation	PFMBench DEEPSOL: DeepSol, DeepSol (PFMBench split)	Not reported	Not reported	0.819 (best in column)	Not reported
ProstT5Evaluation	PFMBench EC: Enzyme Commission, Enzyme Commission (PFMBench split)	Not reported	Not reported	Not reported	0.768 (best in column)
ProstT5Evaluation	PFMBench PDB-BIND: PDBbind, PDBbind (PFMBench split)	Not reported	0.183 (best in column)	Not reported	Not reported
ProstT5Evaluation	PFMBench STABILITY: TAPE_Stability, TAPE_Stability (PFMBench split)	Not reported	0.13	Not reported	Not reported

All 11 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ProstT5	Task: PFMBench ANTI-RES: Antibiotic resistance Dataset subset: Antibiotic resistance (PFMBench split)	0.69 Accuracy fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Anti.Res.)
Configuration: ProstT5	Task: PFMBench BINDING-DB: BindingDB Dataset subset: BindingDB (PFMBench split)	0.166 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Bind. DB)
Configuration: ProstT5	Task: PFMBench CLONING-CLF: Cloning CLF Dataset subset: Cloning CLF (PFMBench split)	0.799 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Clo. CLF)
Configuration: ProstT5	Task: PFMBench DEEPLOC2: DeepLoc2 Multi Dataset subset: DeepLoc2 Multi (PFMBench split)	0.732 F1 max (multi-label; TorchDrug-style F1_score_max) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(DL2 M.)
Configuration: ProstT5	Task: PFMBench DEEPSOL: DeepSol Dataset subset: DeepSol (PFMBench split)	0.819 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(DeepSol)
Configuration: ProstT5	Task: PFMBench EC: Enzyme Commission Dataset subset: Enzyme Commission (PFMBench split)	0.768 F1 max (multi-label; TorchDrug-style F1_score_max) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(EC)
Configuration: ProstT5	Task: PFMBench MAT-PROD: Material production Dataset subset: Material production (PFMBench split)	0 .81622 Accuracy fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Mat.Pro.)
Configuration: ProstT5	Task: PFMBench METAL-ION: Metal ion binding Dataset subset: Metal ion binding (PFMBench split)	0.721 Accuracy fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(M. I. Bin.)
Configuration: ProstT5	Task: PFMBench PDB-BIND: PDBbind Dataset subset: PDBbind (PFMBench split)	0.183 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(PDBBind)
Configuration: ProstT5	Task: PFMBench SEC-STRUCT: Secondary structure Dataset subset: Secondary structure (PFMBench split)	0 .81397 Accuracy fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Sec. Str.)
Configuration: ProstT5	Task: PFMBench STABILITY: TAPE_Stability Dataset subset: TAPE_Stability (PFMBench split)	0.13 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ProstT5 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(ProstT5 [ 21 ]), column(Stability)

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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pfmbench primary benchmark evidence · Original source · 2506.14796v1

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Technical metadata and extraction receipts

Stable ID: pfmbench-method-prostt5

areas: proteins-complexes
source locator: Table 3, row(ProstT5 [ 21 ])
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence-Structure.

Related records

system: ProstT5 on PFMBench ANTI-RES: Antibiotic resistance
system: ProstT5 on PFMBench BINDING-DB: BindingDB
system: ProstT5 on PFMBench CLONING-CLF: Cloning CLF
system: ProstT5 on PFMBench DEEPLOC2: DeepLoc2 Multi
system: ProstT5 on PFMBench DEEPSOL: DeepSol
system: ProstT5 on PFMBench EC: Enzyme Commission
system: ProstT5 on PFMBench MAT-PROD: Material production
system: ProstT5 on PFMBench METAL-ION: Metal ion binding
system: ProstT5 on PFMBench PDB-BIND: PDBbind
system: ProstT5 on PFMBench SEC-STRUCT: Secondary structure
system: ProstT5 on PFMBench STABILITY: TAPE_Stability

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