Identification of protein binding pockets is of importance in structure-based drug design. Protein movement may affect the geometric and physicochemical properties of protein pockets. This server (D3Pockets) is developed to detect and analyze the dynamic properties of ligand binding pockets on drug target protein. It can not only detect all potential ligand binding pockets on protein surface based on a pdb file, but also analyze the dynamic properties of the pockets, viz., stability, continuity and correlation, based on a MD trajectory or a conformation ensemble. The results from the server could be used for designing ligands on novel pockets and studying the functional mechanism of a target protein.
1. Zhaoqiang Chen, Xinben Zhang, Cheng Peng, Jinan Wang, Zhijian Xu, Kaixian Chen, Jiye Shi, Weiliang Zhu, D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. J. Chem. Inf. Model. 2019. DOI:https://doi.org/10.1021/acs.jcim.9b00332