4 papers
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…
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…
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…
FABind: Fast and Accurate Protein-Ligand Binding
Qizhi Pei, Kaiyuan Gao, Lijun Wu +7
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements i…