FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints.

Yueqing Zhang, Zhihan Zhang, Dongliang Ke, Xiaolin Pan, Xingyu Wang, Xudong Xiao, Changge Ji

Journal of chemical information and modeling 2024 May 27

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Fragment growing is an important ligand design strategy in drug discovery. In this study, we present FragGrow, a web server that facilitates structure-based drug design by fragment growing. FragGrow offers two working modes: one for growing molecules through the direct replacement of hydrogen atoms or substructures and the other for growing via virtual synthesis. FragGrow works by searching for suitable fragments that meet a set of constraints from an indexed 3D fragment database and using them to create new compounds in 3D space. The users can set a range of constraints when searching for their desired fragment, including the fragment's ability to interact with specific protein sites; its size, topology, and physicochemical properties; and the presence of particular heteroatoms and functional groups within the fragment. We hope that FragGrow will serve as a useful tool for medicinal chemists in ligand design. The FragGrow server is freely available to researchers and can be accessed at https://fraggrow.xundrug.cn.

Citation

Yueqing Zhang, Zhihan Zhang, Dongliang Ke, Xiaolin Pan, Xingyu Wang, Xudong Xiao, Changge Ji. FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints. Journal of chemical information and modeling. 2024 May 27;64(10):3970-3976