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Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem. (arXiv:2206.04119v1 [q-bio.BM])
June 10, 2022, 1:10 a.m. | Brian L. Trippe, Jason Yim, Doug Tischer, Tamara Broderick, David Baker, Regina Barzilay, Tommi Jaakkola
cs.LG updates on arXiv.org arxiv.org
Construction of a scaffold structure that supports a desired motif,
conferring protein function, shows promise for the design of vaccines and
enzymes. But a general solution to this motif-scaffolding problem remains open.
Current machine-learning techniques for scaffold design are either limited to
unrealistically small scaffolds (up to length 20) or struggle to produce
multiple diverse scaffolds. We propose to learn a distribution over diverse and
longer protein backbone structures via an E(3)-equivariant graph neural
network. We develop SMCDiff to efficiently …
3d arxiv bio diffusion modeling probabilistic modeling protein
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