Benchmarking Peptide-Protein Affinity Prediction Across Peptide and Target Shifts

Abstract

Peptide-protein affinity models are often evaluated with a single data split, obscuring whether they interpolate among measurements for observed targets or generalize across peptide or target shifts. We integrated three sources of quantitative peptide-protein binding data to obtain 11,349 deduplicated pairs and benchmarked ten peptide representations, ESM-2 protein embeddings, and six regressors under peptide-similarity, within-target, and leave-target-out partitions. Across 60 matched representation-regressor configurations, mean test Spearman correlations were 0.462, 0.669, and 0.530, respectively. The top configuration shifted from ECFP-16 count fingerprints with random forest in the first two settings to HELM-BERT with Extra Trees when exact target sequences were excluded. Representation-rank correlations ranged from -0.042 to 0.624 across partitions, whereas regressor-rank correlations ranged from 0.771 to 0.943. Learning curves showed that representation differences were largest with limited supervision and narrowed as training data increased. PeptideCLM-2 adaptation and simple element-wise interaction features provided no consistent gain over a frozen encoder and direct concatenation under the tested protocols. These conclusions are specific to a dataset that pools transformed Kd, Ki, and IC50 measurements and to target exclusion at the exact-sequence level. Peptide-protein affinity benchmarks should therefore align data partitions with the intended use and jointly assess the effects of data scale, molecular representation, and downstream learner.