Decoding protein-protein interactions (PPIs) at the residue level is crucial
for understanding cellular mechanisms and developing targeted therapeutics. We
present Seq2Bind Webserver, a computational framework that leverages fine-tuned
protein language models (PLMs) to determine binding affinity between proteins
and identify critical binding residues directly from sequences, eliminating the
structural requirements that limit most affinity prediction tools. We
fine-tuned four architectures including ProtBERT, ProtT5, ESM2, and BiLSTM on
the SKEMPI 2.0 dataset containing 5,387 protein pairs with experimental binding
affinities. Through systematic alanine mutagenesis on each residue for 14
therapeutically relevant protein complexes, we evaluated each model's ability
to identify interface residues. Performance was assessed using N-factor
metrics, where N-factor=3 evaluates whether true residues appear within 3n top
predictions for n interface residues. ESM2 achieved 49.5% accuracy at
N-factor=3, with both ESM2 (37.2%) and ProtBERT (35.1%) outperforming
structural docking method HADDOCK3 (32.1%) at N-factor=2. Our sequence-based
approach enables rapid screening (minutes versus hours for docking), handles
disordered proteins, and provides comparable accuracy, making Seq2Bind a
valuable prior to steer blind docking protocols to identify putative binding
residues from each protein for therapeutic targets. Seq2Bind Webserver is
accessible at this https URL under StructF suite.