Institute of Computational Science - Center for Computational Medicine in Cardiology, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Lugano CH-6900, Switzerland.
Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
Bioinformatics. 2019 Dec 15;35(24):5328-5330. doi: 10.1093/bioinformatics/btz543.
The ligand/protein binding interaction is typically investigated by docking and molecular dynamics (MD) simulations. In particular, docking-based virtual screening (VS) is used to select the best ligands from database of thousands of compounds, while MD calculations assess the energy stability of the ligand/protein binding complexes. Considering the broad use of these techniques, it is of great demand to have one single software that allows a combined and fast analysis of VS and MD results. With this in mind, we have developed the Drug Discovery Tool (DDT) that is an intuitive graphics user interface able to provide structural data and physico-chemical information on the ligand/protein interaction.
DDT is designed as a plugin for the Visual Molecular Dynamics (VMD) software and is able to manage a large number of ligand/protein complexes obtained from AutoDock4 (AD4) docking calculations and MD simulations. DDT delivers four main outcomes: i) ligands ranking based on an energy score; ii) ligand ranking based on a ligands' conformation cluster analysis; iii) identification of the aminoacids forming the most occurrent interactions with the ligands; iv) plot of the ligands' center-of-mass coordinates in the Cartesian space. The flexibility of the software allows saving the best ligand/protein complexes using a number of user-defined options.
DDT_site_1 (alternative DDT_site_2); the DDT tutorial movie is available here.
Supplementary data are available at Bioinformatics online.
配体/蛋白质结合相互作用通常通过对接和分子动力学 (MD) 模拟来研究。特别是，基于对接的虚拟筛选 (VS) 用于从数千种化合物的数据库中选择最佳配体，而 MD 计算评估配体/蛋白质结合复合物的能量稳定性。考虑到这些技术的广泛应用，非常需要有一种单一的软件，允许对 VS 和 MD 结果进行组合和快速分析。考虑到这一点，我们开发了药物发现工具 (DDT)，它是一个直观的图形用户界面，能够提供配体/蛋白质相互作用的结构数据和物理化学信息。
DDT 被设计为 Visual Molecular Dynamics (VMD) 软件的插件，能够管理从 AutoDock4 (AD4) 对接计算和 MD 模拟中获得的大量配体/蛋白质复合物。DDT 提供了四个主要结果：i）基于能量得分的配体排序；ii）基于配体构象聚类分析的配体排序；iii）鉴定与配体形成最常见相互作用的氨基酸；iv）配体质心坐标在笛卡尔空间中的绘图。该软件的灵活性允许使用许多用户定义的选项保存最佳的配体/蛋白质复合物。
DDT_site_1（替代 DDT_site_2）；DDT 教程电影可在此处查看。
补充数据可在 Bioinformatics 在线获得。
