arXiv:2606. 05198v1 Announce Type: cross Abstract: Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging.
By Shi Li (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Xujun Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Mingquan Liu (Faculty of Health Sciences, University of Macau, Macau SAR, China), Hui Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Shuoying Jia (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Yu Kang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Tingjun Hou (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China), Peichen Pan (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China)
arXiv:2608.20366v1 Announce Type: cross
Abstract: Molecular docking requires reasoning jointly about ligand pose and protein flexibility. Most diffusion-based docking models predict torsional updates...
By Maksim Zhdanov, Pavel Strashnov, Vladislav Kurenkov
arXiv:2607. 17412v1 Announce Type: new Abstract: A hallmark of neurodegenerative diseases such as Alzheimer's and Parkinson's is the aberrant aggregation of proteins into amyloid fibrils, and small molecules that selectively bind to these fibrils hold promise as diagnostics, imaging probes, and therapeutics.
By Yasheng Sun, Bohan Li, Youqi Tao, J\"urgen Schmidhuber
arXiv:2610.04850v2 Announce Type: replace
Abstract: Protein binding prediction is central to target identification, therapeutic binder design, and large scale screening, yet remains challenging becau...
By Jae Won Choi, Ryoonki Hong, Alan Liang, Manjula Adiveppa Wader, Bingsong Zeng, Peiyang Tang, Longwei Liu, Ruishan Liu
Matcha is a new molecular docking method that refines ligand poses through three flow-matching stages—translation, rotation, and torsion—before applying GNINA for minimization, filtering, and ranking. It achieves high physical plausibility and is approximately 28 times faster than current large-scale co‑folding models, outperforming existing benchmarks. The authors provide code, benchmarking artifacts, and model checkpoints on GitHub and Zenodo.
By Daria Frolova, Talgat Daulbaev, Egor Sevriugov, Sergei A. Nikolenko, Dmitry N. Ivankov, Ivan Oseledets, Marina A. Pak
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