DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina
DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina
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DOI：
10.1007/s10822-016-0006-1
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发表时间：
2017-02-01
影响因子：
3.5
通讯作者：
Polticelli, Fabio
中科院分区：
文献类型：
--
作者：
Di Muzio, Elena;Toti, Daniele;Polticelli, Fabio
分子对接是一种强大的技术，它有助于揭示大分子与底物、内源和外源配体以及抑制剂之间相互作用的结构和能量基础。此外，这项技术在加速筛选用于药物开发目的的大型化合物文库方面发挥了关键作用。需要促进社区驱动的药物开发努力，特别是在被忽视的疾病方面，需要方便用户的工具，使非专家使用者能够充分发挥分子对接的潜力。沿着这条道路，这里描述了DockingApp的实现，这是一个免费可用的、极其用户友好的、独立于平台的应用程序，用于使用AutoDock Vina执行对接模拟和虚拟筛选任务。DockingApp拥有直观的图形用户界面，极大地方便了输入阶段和结果分析，使用嵌入式JMOL小程序可以以图形形式可视化结果。该应用程序附带了DrugBank的1400多种可随时对接的FDA批准的药物，以促进虚拟筛查和药物再利用倡议。此外，其他化合物数据库，如锌，也可以AutoDock格式提供，可以很容易地插入。
Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.