Recent, interesting papers

Created on February 06, 2025

2025   ·   Review

Generative models for small molecules

  • Tao, Nianze, and Minori Abe. “Bayesian Flow Network Framework for Chemistry Tasks.” Journal of Chemical Information and Modeling, January 21, 2025, acs.jcim.4c01792. https://doi.org/10.1021/acs.jcim.4c01792.

  • Zhang, Zaixi, Mengdi Wang, and Qi Liu. “FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling.” arXiv, September 29, 2024. https://doi.org/10.48550/arXiv.2409.19645.

  • Lee, Seul, Karsten Kreis, Srimukh Prasad Veccham, Meng Liu, Danny Reidenbach, Yuxing Peng, Saee Paliwal, Weili Nie, and Arash Vahdat. “GenMol: A Drug Discovery Generalist with Discrete Diffusion.” arXiv, January 10, 2025. https://doi.org/10.48550/arXiv.2501.06158.

Molecular Docking

  • Qiao, Zhuoran, Weili Nie, Arash Vahdat, Thomas F. Miller, and Animashree Anandkumar. “State-Specific Protein–Ligand Complex Structure Prediction with a Multiscale Deep Generative Model.” Nature Machine Intelligence 6, no. 2 (February 12, 2024): 195–208. https://doi.org/10.1038/s42256-024-00792-z.

  • Morehead, Alex, and Jianlin Cheng. “FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction.” arXiv, December 14, 2024. https://doi.org/10.48550/arXiv.2412.10966.

  • Lu, Wei, Jixian Zhang, Weifeng Huang, Ziqiao Zhang, Xiangyu Jia, Zhenyu Wang, Leilei Shi, Chengtao Li, Peter G. Wolynes, and Shuangjia Zheng. “DynamicBind: Predicting Ligand-Specific Protein-Ligand Complex Structure with a Deep Equivariant Generative Model.” Nature Communications 15, no. 1 (February 5, 2024): 1071. https://doi.org/10.1038/s41467-024-45461-2.