Scalable Peptide Design via Memory-Efficient Equivariant Transformer

Engineering notes

Engineering notes will be added by the aipentium editorial team.

Chinese explanation / 中文解读

中文解读待补充：本站会优先为大语言模型、生成式AI、ChatGPT相关技术、计算机视觉、深度学习等高价值论文补充中文说明。

Original abstract

Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this problem by compressing fine grained atomic structures into block level latent representations and performing conditional generation in a compact latent space. However, the scalability of such systems depends heavily on the geometric backbone used throughout their encoding, decoding, and denoising components. We introduce MEET (Memory Efficient Equivariant Transformer), an E(3) equivariant backbone for scalable atomistic peptide modeling. MEET maintains coupled invariant scalar and equivariant vector feature streams, while reformulating geometric computation around memory efficient attention. It initializes vector features through global coordinate aggregation, incorporates pairwise distances through augmented query and key dot products, and injects covalent bond information through sparse bond adaptation. Integrated into a VAE and latent diffusion pipeline for full atom peptide generation, \model{} achieves linear memory scaling with atom count and improves generation quality over existing peptide design methods. Experiments on large scale AFDB derived datasets further show that the proposed backbone supports systematic model and data scaling, leading to better binding affinity, physical validity, and sample diversity.

Links and sources

• Official / arXiv page
• PDF from original source

Comments