A systematic benchmark and architecture comparison shows that hierarchical pooling and pooled cross-attention usually beat concatenation for PLM-based protein-protein binding affinity prediction, although statistical significance is not established.
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions
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Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction
A systematic benchmark and architecture comparison shows that hierarchical pooling and pooled cross-attention usually beat concatenation for PLM-based protein-protein binding affinity prediction, although statistical significance is not established.