From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

Existing protein geometry models typically represent molecular surfaces using local geometric features such as sampled points, normals, and curvature. While effective for capturing exposed molecular shape, these representations do not explicitly model the volumetric organization beneath the surface or provide a consistent coordinate system for residue-wise volumetric structure. We introduce Protein-TetSphere, a registered residue-wise volumetric representation for proteins. Each protein chain is tetrahedralized to obtain local volumetric regions associated with individual residues, which are then registered to a shared fixed-topology tetrahedral reference and represented in a common Laplacian basis. This registration establishes consistent volumetric coordinates across residues, enabling local three-dimensional deformation to be integrated with surface and chemical information in a multimodal protein representation. We evaluate Protein-TetSphere on ligand-binding pocket classification, protein--protein interface prediction, and de novo protein binder design. Across the three tasks, Protein-TetSphere improves ligand-binding pocket balanced accuracy from 0.795 to 0.826, Pinder-Pair/Site AUROC from 0.914/0.852 to 0.932/0.866, and binder-design success from 14.95% to 19.90% on the BoltzGen Challenge Set and from 27.62% to 32.19% at the ProtDBench backbone level. These results show that registered volumetric geometry provides complementary spatial information beyond molecular surfaces across protein recognition, interaction, and design.