The Internet

Docking (animal)

Biochemistry

Virtual screening

Bioinformatics

Protein Data Bank (RCSB PDB)

Biology

Binding site

Operating system

Computer science

Macromolecular docking

Nursing

Computational biology

Drug discovery

Web server

DOCK

Medicine

Protein–ligand docking

Nucleic Acids Research

Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. 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. 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. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. 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. The web server is freely available at https://cadd.labshare.cn/cb-dock2/.

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