Poster
ProtPainter: Draw or Drag Protein via Topology-guided Diffusion
Zhengxi Lu · Shizhuo Cheng · Yuru Jiang · Yan Zhang · Min Zhang
Hall 3 + Hall 2B #6
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Abstract
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Sat 26 Apr midnight PDT
— 2:30 a.m. PDT
Abstract:
Recent advances in protein backbone generation have achieved promising results under structural, functional, or physical constraints. However, existing methods lack the flexibility for precise topology control, limiting navigation of the backbone space. We present ProtPainter, a diffusion-based approach for generating protein backbones conditioned on 3D curves. ProtPainter follows a two-stage process: curve-based sketching and sketch-guided backbone generation. For the first stage, we propose CurveEncoder, which predicts secondary structure annotations from a curve to parametrize sketch generation. For the second stage, the sketch guides the generative process in Denoising Diffusion Probabilistic Modeling (DDPM) to generate backbones. During the process, we further introduce a fusion scheduling scheme, Helix-Gating, to control the scaling factors. To evaluate, we propose the first benchmark for topology-conditioned protein generation, introducing Protein Restoration Task and a new metric, self-consistency Topology Fitness (scTF). Experiments demonstrate ProtPainter's ability to generate topology-fit (scTF > 0.8) and designable (scTM > 0.5) backbones, with drawing and dragging tasks showcasing its flexibility and versatility.
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