3 papers
q-bio.BM2025
CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions
Yangzhe Peng, Kaiyuan Gao, Liang He +4
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond betwe…
q-bio.BM2025
FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation
Kaiyuan Gao, Qizhi Pei, Gongbo Zhang +3
Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are…
cs.LG2024
Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
Kaiyuan Gao, Yusong Wang, Haoxiang Guan +5
The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics…