Biomolecules

Generative Replica-Exchange: A Flow-based Framework for Accelerating Replica Exchange Simulations Shengjie Huang, Sijie Yang, Jianqiao Yi, Rui Zheng, Haocong Liao, Muzammal Hussain, Yaoquan Tu, … arxiv.org/abs/2603.18076 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚌𝚘𝚖𝚙-𝚙𝚑]

Integrative modelling of protein-glycan interactions with HADDOCK3 Victor Reys, Marco Giulini, Alexandre M. J. J. Bonvin arxiv.org/abs/2603.17251 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics Liang Shi, Jiarui Lu, Junqi Liu, Chence Shi, Zhi Yang, Jian Tang arxiv.org/abs/2603.17633 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

Training a force field for proteins and small molecules from scratch Alexandre Blanco-González, Thea K Schulze, Evianne Rovers, Joe G Greener arxiv.org/abs/2603.16770 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Topological Enhancement of Protein Kinetic Stability João NC Especial, Patrícia FN Faísca arxiv.org/abs/2603.12053 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Joint Geometric-Chemical Distance for Protein Surfaces Himanshu Swami, John M. McBride, Jean-Pierre Eckmann, Tsvi Tlusty arxiv.org/abs/2603.09860 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚋𝚒𝚘-𝚙𝚑]

Preservation Constraints on aDNA Information Generation and the HSF Posterior Sourcing Framework: A First-Principles Critique of Conventional Methods Wan-Qian Zhao, Shu-Jie Zhang, Zhan-Yong Guo, Mei-Jun Li arxiv.org/abs/2603.07137 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Sampling-based Continuous Optimization for Messenger RNA Design Feipeng Yue, Ning Dai, Wei Yu Tang, Tianshuo Zhou, David H. Mathews, Liang Huang arxiv.org/abs/2603.06559 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Fast and Versatile RNA Design via Motif-level Divide-and-Conquer and Structure-level Rival Search Tianshuo Zhou, David H. Mathews, Liang Huang arxiv.org/abs/2603.02283 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Exploring Drug Safety Through Knowledge Graphs: Protein Kinase Inhibitors as a Case Study David Jackson, Michael Gertz, Jürgen Hesser arxiv.org/abs/2603.00097 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸 𝚌𝚜.𝙲𝙴 𝚌𝚜.𝙸𝚁 𝚌𝚜.𝙻𝙶]

Bi-TEAM: A Unified Cross-Scale Representation Learning Framework for Chemically Modified Biomolecules Chunbin Gu, Zijun Gao, Mutian He, Jingjie Zhang, Haipeng Wen, Zihao Luo, Xiaorui Wang, Hanqun Cao, Jiajun Bu, Chang-Yu Hsieh, … arxiv.org/abs/2603.01873 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Inference-time optimization for experiment-grounded protein ensemble generation Advaith Maddipatla, Anar Rzayev, Marco Pegoraro, Martin Pacesa, Paul Schanda, Ailie Marx, Sanketh Vedula, Alex M. Bronstein arxiv.org/abs/2602.24007 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints Fuyao Huang, Xiaozhu Yu, Kui Xu, Qiangfeng Cliff Zhang arxiv.org/abs/2602.22263 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸 𝚎𝚎𝚜𝚜.𝙸𝚅 𝚚-𝚋𝚒𝚘.𝚀𝙼]

Spectral entropy of the discrete Hasimoto effective potential exposes sub-residue geometric transitions in protein secondary structure Yiquan Wang arxiv.org/abs/2602.21787 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚖𝚊𝚝𝚑-𝚙𝚑 𝚖𝚊𝚝𝚑.𝙼𝙿 𝚗𝚕𝚒𝚗.𝙿𝚂 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚋𝚒𝚘-𝚙𝚑]

Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design Ziyi Yang, Zitong Tian, Yinjun Jia, Tianyi Zhang, Jiqing Zheng, Hao Wang, Yubu Su, Juncai He, Lei Liu, Yanyan Lan arxiv.org/abs/2602.20176 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

BioLM-Score: Language-Prior Conditioned Probabilistic Geometric Potentials for Protein-Ligand Scoring Zhangfan Yang, Baoyun Chen, Dong Xu, Jia Wang, Ruibin Bai, Junkai Ji, Zexuan Zhu arxiv.org/abs/2602.18476 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸 𝚌𝚜.𝙻𝙶]

Metrology of Complexity and Implications for the Study of the Emergence of Life Sara Imari Walker arxiv.org/abs/2602.18203 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

A Mathematical Theory of Redox Biology James N. Cobley, Michalis G. Nikolaidis arxiv.org/abs/2602.08897 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Somatic Mechanotherapy Activates a Spatiotemporally Synchronized CPTC Wnt Axis for Gut Regeneration Haixiang Huang, Zhenwei Zhang, BingBing Shen, Jianming Yue, Lu Mei, Xudong Zhu, Yonghong Shi, Qianmei Zhu, Yeping Shi, Yifan Luo, … arxiv.org/abs/2602.05451 [𝚚-𝚋𝚒𝚘.𝙱𝙼]

Generative AI for Enzyme Design and Biocatalysis Lasse Middendorf, Noelia Ferruz arxiv.org/abs/2602.03779 [𝚚-𝚋𝚒𝚘.𝙱𝙼]