arXiv:2606. 25006v1 Announce Type: new Abstract: Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints.
By Rui Jiao, Xiangzhe Kong, Yinjun Jia, Yijia Zhang, Ziyi Yang, Yang Liu, Jianzhu Ma
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.
TorchCraft is a unified binder‑design framework that optimizes sequence logits using a frozen all‑atom structure predictor. It integrates confidence, contact, geometric, and sequence‑prior objectives within TorchFold to design minibinders, framework‑conditioned VHHs, cyclic peptides, and ligand‑binding proteins. Using pretrained AlphaFold 3 weights, TorchCraft produced experimentally validated binders across four targets without post‑hoc redesign, and computational tests confirmed its applicability to cyclic peptides and ligand‑conditioned pocket design.
By TorchCraft Team, Yu Liu, Zhouhanyu Shen, Zhengyi Li, Xikun Huang, Jiaqi Liu, Shuxian Gao, Qilin Yu, Xiayan Qin, Yucheng Zhang, Mingchen Chen
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
By Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
arXiv:2607. 05736v1 Announce Type: new Abstract: Molecular property prediction often relies on isolated data modalities, where continuous 3D graph neural networks (GNNs) struggle to efficiently capture long-range topological dependencies and exact macroscopic heuristics.
By Qiwei Han, Chi Zhou, Ruobing Wang, Zheng Ma
arXiv:2607. 12380v1 Announce Type: new Abstract: Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture.
By Yuxuan Ren, Fan Yang, Jianhua Yao, Yatao Bian