Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Methods Mol Biol. 2024;2714:113-125. doi: 10.1007/978-1-0716-3441-7_6.
Protein-ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and biological research. Recently, our new blind docking server named CB-Dock2 has been released and is currently being utilized by researchers worldwide. CB-Dock2 outperforms state-of-the-art methods due to its accuracy in binding site identification and binding pose prediction, which are enabled by its knowledge-based docking engine. This highly automated server offers interactive and intuitive input and output web interfaces, making it an efficient and user-friendly tool for the bioinformatics and cheminformatics communities. This chapter provides a brief overview of the methods, followed by a detailed guide on using the CB-Dock2 server. Additionally, we present a case study that evaluates the performance of protein-ligand blind docking using this tool.
蛋白质配体盲对接是一种广泛应用于药物和生物研究中研究配体和受体结合位点和构象的方法。最近，我们发布了一个名为 CB-Dock2 的新的盲对接服务器，目前正在被全球的研究人员使用。CB-Dock2 由于其基于知识的对接引擎在识别结合位点和预测结合构象方面的准确性而优于最先进的方法。这个高度自动化的服务器提供了交互式和直观的输入和输出网络界面，使其成为生物信息学和化学信息学社区的一个高效和用户友好的工具。这一章简要介绍了该方法，随后详细介绍了如何使用 CB-Dock2 服务器。此外，我们还展示了一个案例研究，评估了使用该工具进行蛋白质配体盲对接的性能。
