Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion

Yutong Hu, Yang Tan, Andi Han, Lirong Zheng, Liang Hong, Bingxin Zhou

Keywords: latent diffusion model; protein sequence generation; graph neural networks; protein language model

TL;DR: We propose a latent graph diffusion model for generating novel and diverse protein sequences based on secondary structures.

Abstract: The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing methods face challenges in generating proteins with diverse lengths and shapes while maintaining key structural features. To address these challenges, we introduce CPDiffusion-SS, a latent graph diffusion model that generates protein sequences based on coarse-grained secondary structural information. CPDiffusion-SS offers greater flexibility in producing a variety of novel amino acid sequences while preserving overall structural constraints, thus enhancing the reliability and diversity of generated proteins. Experimental analyses demonstrate the significant superiority of the proposed method in producing diverse and novel sequences, with CPDiffusion-SS surpassing popular baseline methods on open benchmarks across various quantitative measurements. Furthermore, we provide a series of case studies to highlight the biological significance of the generation performance by the proposed method.

Submission Number: 192