| Literature DB >> 31265282 |
Zhaoqiang Chen1,2, Xinben Zhang1, Cheng Peng1,2, Jinan Wang1, Zhijian Xu1,2, Kaixian Chen1,2,3, Jiye Shi4, Weiliang Zhu1,2,3.
Abstract
The intrinsic dynamic properties of the ligand-binding pockets of proteins are important for the protein function mechanism and thus are useful to drug discovery and development. Few methods are available to study the dynamic properties, such as pocket stability, continuity, and correlation. In this work, we develop a method and web server, namely, D3Pockets, for exploring the dynamic properties of the protein pocket based on either molecular dynamics (MD) simulation trajectories or conformational ensembles. Application of D3Pockets on five target proteins as examples, namely, HIV-1 protease, BACE1, L-ABP, GPX4, and GR, uncovers more information on the dynamic properties of the ligand-binding pockets, which should be helpful to understanding protein function mechanism and drug design. The D3Pockets web server is available at http://www.d3pharma.com/D3Pocket/index.php .Entities:
Year: 2019 PMID： 31265282 DOI： 10.1021/acs.jcim.9b00332
Source DB: PubMed Journal: J Chem Inf Model ISSN： 1549-9596 Impact factor: 4.956