A Large-Scale Dataset and Benchmark: Do Protein-Ligand Models Learn Binding Sites or Just Binding Likelihood?

arXiv:2605.24045v1 Announce Type: new Abstract: Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition.