{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/improved-motif-scaffolding-with-se-3-flow","title":"Improved motif-scaffolding with SE(3) flow matching","arxiv_id":"2401.04082","date":"2024-01-08","proceeding":null,"authors":["Jason Yim","Andrew Campbell","Emile Mathieu","Andrew Y. K. Foong","Michael Gastegger","José Jiménez-Luna","Sarah Lewis","Victor Garcia Satorras","Bastiaan S. Veeling","Frank Noé","Regina Barzilay","Tommi S. Jaakkola"],"abstract":"Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success in designing scaffolds for a range of motifs. However, generated scaffolds tend to lack structural diversity, which can hinder success in wet-lab validation. In this work, we extend FrameFlow, an SE(3) flow matching model for protein backbone generation, to perform motif-scaffolding with two complementary approaches. The first is motif amortization, in which FrameFlow is trained with the motif as input using a data augmentation strategy. The second is motif guidance, which performs scaffolding using an estimate of the conditional score from FrameFlow without additional training. On a benchmark of 24 biologically meaningful motifs, we show our method achieves 2.5 times more designable and unique motif-scaffolds compared to state-of-the-art. 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