Protocol

DeepProtein PPI affinity (PEER): R2 ↑

Protein-protein binding affinity regression. Scored by coefficient of determination.

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.

11 recorded evaluations, 11 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

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

Protocol: DeepProtein PPI affinity (PEER): R2 ↑ · Dataset: PPI affinity (PEER)

Sorted by R² (coefficient of determination) (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	R² (coefficient of determination)
CNN (DeepProtein benchmark)Evaluation	0.646±0.003 (best in column)
Deep Prot-T5 (DeepProtein benchmark)Evaluation	0.643
ESM-2-650M (DeepProtein benchmark)Evaluation	0.592 ± 0.001
CNN-RNN (DeepProtein benchmark)Evaluation	0.584 ± 0.026
Prot-T5-XL (DeepProtein benchmark)Evaluation	0.573 ± 0.011
Transformer (DeepProtein benchmark)Evaluation	0.425±0.021
GCN (DeepProtein benchmark)Evaluation	0.366±0.034
GAT (DeepProtein benchmark)Evaluation	0.230±0.001
NeuralFP (DeepProtein benchmark)Evaluation	0.100±0.054
ChemLLM-7B (DeepProtein benchmark)Evaluation	0.082
LlaSMol-Mistral-7B (DeepProtein benchmark)Evaluation	−0.008

All 11 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: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.082 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source 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 ChemLLM-7B 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 'ChemLLM-7B', column group 'PPI Affinity', column 'R2 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.646±0.003 R² (coefficient of determination) 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 CNN 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 'CNN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.584 ± 0.026 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.026 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 CNN-RNN 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 'CNN-RNN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.643 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source 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 Deep Prot-T5 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 'Deep Prot-T5', column group 'PPI Affinity', column 'R2 ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.592 ± 0.001 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.001 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 ESM-2-650M 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 'ESM-2-650M', column group 'PPI Affinity', column 'R2 ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.230±0.001 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.001 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 GAT 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 'GAT', column group 'PPI Affinity', column 'R2 ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.366±0.034 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.034 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 GCN 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 'GCN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	−0.008 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source 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 LlaSMol-Mistral-7B 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 'LlaSMol-Mistral-7B', column group 'PPI Affinity', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.100±0.054 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.054 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 NeuralFP 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 'NeuralFP', column group 'PPI Affinity', column 'R2 ↑'
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: Transformer (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.425±0.021 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.021 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 Transformer 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 'Transformer', column group 'PPI Affinity', column 'R2 ↑'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 11

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set mean where supervised fitting is permitted

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Simple features with train-only ridge regression

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

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

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2

areas: protein-function
contexts: research
protocol: Train on the task's training split and score PPI affinity (PEER) on its test split; five random seeds per method, mean and standard deviation reported.
metric: coefficient-of-determination
metric direction: higher
unit: unitless
metric qualifier: coefficient of determination
version: As published 2025
source locator: PPI affinity (PEER): column 'R2 ↑' of its table in Tables 2 to 8
replicates: Five random seeds (table footnote a: 'we used five different random seeds to perform independent runs, reporting the average results along with their standard deviations')
limitations: Author-reported results: the DeepProtein authors ran every method.
dataset: PPI affinity (PEER); train/valid/test 2127/212/343

Related records

part of: DeepProtein benchmark
uses data: PPI affinity (PEER)
assessment: ChemLLM-7B on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: CNN on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: CNN-RNN on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: Deep Prot-T5 on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: ESM-2-650M on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: GAT on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: GCN on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: LlaSMol-Mistral-7B on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: NeuralFP on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: Prot-T5-XL on DeepProtein PPI affinity (PEER) (R2 ↑)
assessment: Transformer on DeepProtein PPI affinity (PEER) (R2 ↑)

Suggest a correction