Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning

Many processes in biology and drug discovery involve various 3D interactions between molecules, such as protein and protein, protein and small molecule, etc. Given that different molecules are usually represented in different granularity, existing methods usually encode each type of molecules independently with different models, leaving it defective to learn the universal underlying interaction physics. In this paper, we first propose to universally represent an arbitrary 3D complex as a geometric graph of sets, shedding light on encoding all types …

biology cs.lg discovery drug discovery encode etc interactions learn molecules processes protein q-bio.bm small transformer type