Implicitly and Differentiably Representing Protein Surfaces and Interfaces (2508.11641v1)

Abstract: We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to render images of proteins, it has not, to our knowledge, been widely adopted in a machine learning setting. Mirroring recent successful work applying SDFs to represent 3D geometry, we present a proof of concept that this representation of proteins could be useful in several biologically relevant applications. We also propose further experiments that are necessary to validate the proposed approach.