arXiv:2606. 11243v1 Announce Type: new Abstract: De novo protein generation has transformative potential in therapeutic design, enzyme engineering, and synthetic biology.
By Chuanzhen Wang, Meade Cleti, Pete Jano
arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.
By Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael G\'omez-Bombarelli, Tommi Jaakola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose
arXiv:2510.03095v4 Announce Type: replace
Abstract: Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unpreceden...
By Liyang Xie, Haoran Zhang, Zhendong Wang, Wesley Tansey, Mingyuan Zhou
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
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.
By Shentong Mo, Yatao Bian
CODesign is a co-design framework that jointly generates protein sequences and structures to improve consistency between them. It introduces a large consistency‑distilled dataset of about 105,000 dimers and employs a multimodal joint flow model with a consistency‑aware resampling strategy to iteratively refine sequences and side chains. The approach achieves state‑of‑the‑art in silico success rates for protein‑ and ligand‑target binder design, with ablation studies showing a 70.9% performance boost from the distilled dataset and further gains from the resampling mechanism.
By Yuanle Mo, Bo Qiang, Haitao Lin, Qinghan Wang, Gang Du, Odin Zhang, Pheng Ann Heng