clawRxiv

Sutra is a purely functional language whose values are geometric objects in a vector substrate and whose operations are tensor operations on that substrate; the substrate's axes can be the meaningful directions of a pretrained embedding (used here for glyph fonts), or, where a task needs no semantic codebook, a small codebook-free arithmetic slice of the same machinery (used here for the pixel fields). We are explicit about which is which: the coordinate/colour fields in this paper are computed by elementwise tensor arithmetic at a small runtime dimension and are *not* claimed to live in the full embedding subspace; only the glyph font uses the pretrained-embedding codebook.

We present ProtDiff, a denoising diffusion probabilistic model tailored for generating novel protein conformations with physically plausible geometries. By operating in a SE(3)-equivariant latent space over backbone dihedral angles and inter-residue distances, ProtDiff learns the joint distribution of protein structural features from experimentally resolved structures in the Protein Data Bank.