arXiv:2608. 17381v1 Announce Type: cross Abstract: Biomolecular design underpins applications from molecular recognition to therapeutics and synthetic biology, yet de novo interaction design remains challenging-especially for DNA/RNA, underexplored non-protein modalities with scarce, heterogeneous complex data and sharper geometric and chemical constraints.
By Xuefeng Liu, Mingxuan Cao, Xiao Luo, Songhao Jiang, Tobin Sosnick, Jinbo Xu, Louis Maher, Rick Stevens
arXiv:2608. 07078v1 Announce Type: cross Abstract: Flexible macromolecular docking offers high-fidelity predictions of biomolecular interactions, but remains prohibitively expensive at scale.
By Xiangyu Meng, Peng Chen, Mingzhen Li, Jianmin Wang, Sen Wang, Guangming Tan, Weile Jia, Mohamed Wahib, Tao Luo, Xun Wang
arXiv:2506. 20686v2 Announce Type: replace-cross Abstract: Recent advances in biomolecular modeling have been catalyzed by models such as AlphaFold3 (AF3), which introduce science-informed changes to the transformer architecture.
By Hoa La, Ahan Gupta, Alex Morehead, Jianlin Cheng, Minjia Zhang
arXiv:2607. 19519v1 Announce Type: cross Abstract: Most 3D properties relevant to molecular design, including free energies and shape descriptors, are $\textit{expectations}$ over the Boltzmann distribution over 3D configurations of a molecular graph.
By Selma Moqvist, Richard Beckmann, Ross Irwin, Roc\'io Mercado, Simon Olsson
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
arXiv:2606. 07239v1 Announce Type: new Abstract: The success of generative molecular design hinges on a model's steerability toward high-reward samples.
By Malte Franke, Stefan P. Schmid, Zarko Ivkovic, Kjell Jorner, Andreas Krause