Configuration

Prot-T5-XL (DeepProtein benchmark)

Configuration of Prot-T5-XL: protein language model; default DeepProtein configuration.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

26 evaluations · 26 results. Different protocols are not a single leaderboard.

Sorted by MAE (mean absolute error) (lower 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	MAE (mean absolute error)	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)	AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)	R² (coefficient of determination)	Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)	Accuracy (accuracy, printed on a 0 to 100 scale)
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: MAE ↓, CRISPR-Leenay repair outcome	0.1186 ± 0.0006 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.136 ± 0.003	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: MAE ↓, SAbDab-Chen antibody developability	0.229 ± 0.003	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	0.272 ± 0.030	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	0.535 ± 0.006	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): MAE ↓, PPI affinity (PEER)	1.979 ± 0.007	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: MAE ↓, TAP antibody developability	2.417 ± 0.056	Not reported	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	Not reported	Not reported	Not reported	0.756 ± 0.003	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): Averaged F1 ↑, Binary localization (PEER)	Not reported	93.48 ± 0.07% (best in column)	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): PR-AUC ↑, Binary localization (PEER)	Not reported	Not reported	97.03 ± 0.13% (best in column)	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: R2 ↑, CRISPR-Leenay repair outcome	Not reported	Not reported	Not reported	0.236 ± 0.004	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	Not reported	Not reported	Not reported	0.553 ± 0.003	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Acc ↑, Fold classification (TAPE)	Not reported	Not reported	Not reported	Not reported	Not reported	50.28 ± 0.52%
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Averaged F1 ↑, Fold classification (TAPE)	Not reported	24.24 ± 0.48%	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): Averaged F1 ↑, Human PPI (PEER)	Not reported	87.64 ± 0.98%	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): PR-AUC ↑, Human PPI (PEER)	Not reported	Not reported	95.36 ± 0.07%	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): R2 ↑, PPI affinity (PEER)	Not reported	Not reported	Not reported	0.573 ± 0.011	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: R2 ↑, SAbDab-Chen antibody developability	Not reported	Not reported	Not reported	0.596 ± 0.011	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	62.75 ± 0.76%	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	74.95 ± 1.01%	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	Not reported	Not reported	Not reported	0.767±0.008 (best in column)	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Acc ↑, Subcellular localization (PEER)	Not reported	Not reported	Not reported	Not reported	Not reported	80.67 ± 0.04% (best in column)
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Averaged F1 ↑, Subcellular localization (PEER)	Not reported	69.86 ± 0.39%	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: R2 ↑, TAP antibody developability	Not reported	Not reported	Not reported	0.837 ± 0.010 (best in column)	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): Averaged F1 ↑, Yeast PPI (PEER)	Not reported	66.97 ± 0.01%	Not reported	Not reported	Not reported	Not reported
Prot-T5-XL (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): PR-AUC ↑, Yeast PPI (PEER)	Not reported	Not reported	69.84 ± 0.46%	Not reported	Not reported	Not reported

All 26 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.136 ± 0.003 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein beta-lactamase (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-beta-lactamase-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'β-lactamase', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.756 ± 0.003 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein beta-lactamase (PEER) (ρ ↑) lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'β-lactamase', column 'ρ ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑ Dataset: Binary localization (PEER)	93.48 ± 0.07% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Binary localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-binary-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Prot-T5-XL', column group 'Binary', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑ Dataset: Binary localization (PEER)	97.03 ± 0.13% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Binary localization (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-binary-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Prot-T5-XL', column group 'Binary', column 'PR-AUC ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓ Dataset: CRISPR-Leenay repair outcome	0.1186 ± 0.0006 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.0006 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein CRISPR-Leenay repair outcome (MAE ↓) lit-protein-20261011-deepprotein-protocol-crispr-leenay-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'CRISPR-Leenay', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑ Dataset: CRISPR-Leenay repair outcome	0.236 ± 0.004 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein CRISPR-Leenay repair outcome (R2 ↑) lit-protein-20261011-deepprotein-protocol-crispr-leenay-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'CRISPR-Leenay', column 'R2 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	0.535 ± 0.006 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Fluorescence (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-fluorescence-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Fluorescence', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.553 ± 0.003 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Fluorescence (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-fluorescence-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Fluorescence', column 'ρ ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Acc ↑ Dataset: Fold classification (TAPE)	50.28 ± 0.52% Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.52 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Fold classification (TAPE) (Acc ↑) lit-protein-20261011-deepprotein-protocol-fold-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'Prot-T5-XL', column group 'Fold', column 'Acc ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Averaged F1 ↑ Dataset: Fold classification (TAPE)	24.24 ± 0.48% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.48 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Fold classification (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-fold-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'Prot-T5-XL', column group 'Fold', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	87.64 ± 0.98% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.98 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	95.36 ± 0.07% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.979 ± 0.007 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein PPI affinity (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-ppi-affinity-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'PPI Affinity', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.573 ± 0.011 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: MAE ↓ Dataset: SAbDab-Chen antibody developability	0.229 ± 0.003 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein SAbDab-Chen antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-sabdab-chen-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'SAbDab-Chen', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: R2 ↑ Dataset: SAbDab-Chen antibody developability	0.596 ± 0.011 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein SAbDab-Chen antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-sabdab-chen-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'SAbDab-Chen', column 'R2 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	62.75 ± 0.76% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.76 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Solubility (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-solubility-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	74.95 ± 1.01% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Solubility (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-solubility-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Solubility', column 'PR-AUC ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	0.272 ± 0.030 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.030 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Stability (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-stability-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Stability', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	0.767±0.008 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.008 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Stability (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-stability-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Prot-T5-XL', column group 'Stability', column 'ρ ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Acc ↑ Dataset: Subcellular localization (PEER)	80.67 ± 0.04% Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Subcellular localization (PEER) (Acc ↑) lit-protein-20261011-deepprotein-protocol-subcellular-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Acc ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑ Dataset: Subcellular localization (PEER)	69.86 ± 0.39% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.39 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Subcellular localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: MAE ↓ Dataset: TAP antibody developability	2.417 ± 0.056 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.056 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein TAP antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-tap-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'TAP', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: R2 ↑ Dataset: TAP antibody developability	0.837 ± 0.010 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.010 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein TAP antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-tap-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Prot-T5-XL', column group 'TAP', column 'R2 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	66.97 ± 0.01% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Prot-T5-XL on DeepProtein Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Yeast PPI', column 'Averaged F1 ↑'

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DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)

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Stable ID: lit-protein-20261011-deepprotein-config-prot-t5-xl

areas: protein-function
contexts: research
method types: foundation_model
reported name: Prot-T5-XL
reported configuration: protein language model; default DeepProtein configuration (Table 9)
model identity note: Table 8 prints 'Prot-T5' and Tables 2 to 7 print 'Prot-T5-XL'. They are kept as separate configurations because the article does not state that they are the same checkpoint; their values must not be pooled.
foundation model eligible: true
source locator: Tables 2 to 8, row 'Prot-T5-XL'; Table 9 for the default configuration
missing metadata: version: reason: unreported; note: The tables name the model without a release version
provenance note: Prot-T5-XL as trained and evaluated in the DeepProtein benchmark (protein language model).

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