CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting

Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities.

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• 1 It has seen wide applications in pharmaceutical and biological researches.
• 2 Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019.
• 3 Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction.

Understanding this could lead to better treatments, improved diagnostics, or a deeper grasp of how the human body works — benefiting patient care globally.

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