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DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

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Abstract

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.

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Notes

  1. https://www.chemaxon.com/products/marvin/molconverter/.

  2. It must be noted that affinity is the term used in the Autodock Vina output to indicate the predicted binding energy (lower values indicating tighter binding).

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    Authors and Affiliations

    1. Department of Sciences, Roma Tre University, Rome, Italy

      Elena Di Muzio, Daniele Toti & Fabio Polticelli

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    1. Elena Di Muzio
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    2. Daniele Toti
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    3. Fabio Polticelli
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    Correspondence to Fabio Polticelli.

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    E. Di Muzio and D. Toti have contributed equally to this work.

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    Di Muzio, E., Toti, D. & Polticelli, F. DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina. J Comput Aided Mol Des 31, 213–218 (2017). https://doi.org/10.1007/s10822-016-0006-1

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    • DOI: https://doi.org/10.1007/s10822-016-0006-1

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