arXiv:2607. 15309v1 Announce Type: cross Abstract: Proteins function through coordinated motion across multiple spatial and temporal scales, underpinning processes such as ligand binding, allostery, and catalysis.
By Kaihui Cheng, Zhiqiang Cai, Peng Tu, Yisong Yao, Limei Han, Libo Wu, Siyu Zhu, Tzuhsiung Yang, Yuan Qi
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
By Viet Thanh Duy Nguyen, John K. Johnstone, Truong-Son Hy
arXiv:2512. 18454v3 Announce Type: replace Abstract: Predictive machine learning models generally excel on in-distribution data, but their performance degrades on out-of-distribution (OOD) inputs.
By David Graber, Victor Armegioiu, Rebecca Buller, Siddhartha Mishra
arXiv:2608. 09099v1 Announce Type: new Abstract: Quantitative estimation of protein-ligand binding affinity from three-dimensional complex structures is a fundamental task in structure-based computational chemistry and molecular modeling.
By Qingyang Zou, Jiaye Huang, Hangbo Xie, Jiayue Yin, Youyi Song, Jinfeng Liu
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:2603. 19636v2 Announce Type: replace Abstract: Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce.
By Zhou Zhang, Hanqun Cao, Cheng Tan, Fang Wu, Pheng Ann Heng, Tianfan Fu