Fragment Condition Search

Fragment-based drug design is a proven strategy for discovering high-quality leads. We present FDB&FragLinker, an integrated database and covalent optimization tool that enables users to explore, modify, and reassemble molecular fragments from DrugBank and a large subset of the ZINC database (800M molecules). FragLinker is the first 3D complex generation tool based on fragment-level, allowing precise attachment of selected fragments onto small molecules at designated connection atoms via covalent docking, generating high-quality 3D protein-optimized ligand complex structures.

This approach yields greater structural fidelity than traditional docking and is markedly faster than recent diffusion-based generative models. It can be widely applied to the optimization and modification of small molecules, PROTAC, small molecule polypeptides, etc.