PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS.

Journal of Chemical Information and Modeling
Enade P IstyastonoSudi Mungkasi

Abstract

We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF HIPPOS speeds up the computational times by separating the reference generation and docking analysis. PyPLIF HIPPOS also offers more options compared to PyPLIF. PyPLIF HIPPOS for Linux is stored as the Supporting Information in this application note and can be accessed in GitHub (https://github.com/radifar/PyPLIF-HIPPOS). Additionally, we present here the application of the tool in a retrospective structure-based virtual screening campaign targeting neuraminidase.

References

May 31, 2002·Acta Crystallographica. Section D, Biological Crystallography·Helen M BermanChristine Zardecki
Jan 24, 2007·Journal of Chemical Information and Modeling·Gilles Marcou, Didier Rognan
Jan 8, 2009·Journal of Chemical Information and Modeling·Oliver KorbThomas E Exner
Jun 29, 2011·Topics in Current Chemistry·Didier Rognan
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Jun 22, 2012·Journal of Medicinal Chemistry·Michael M MysingerBrian K Shoichet
Oct 20, 2012·Journal of Chemical Information and Modeling·Roberto TodeschiniPeter Willett
Nov 13, 2012·Journal of Chemical Information and Modeling·Francesco SirciChris de Graaf
Apr 6, 2013·Bioinformation·Muhammad RadifarEnade Perdana Istyastono
May 30, 2013·British Journal of Pharmacology·A J KooistraC de Graaf
Oct 26, 2013·Advances in Experimental Medicine and Biology·Albert J KooistraChris de Graaf
Jun 14, 2014·Progress in Biophysics and Molecular Biology·Sebastian SalentinMichael Schroeder
Oct 26, 2016·Journal of Computer-aided Molecular Design·Philip PrathipatiKenji Mizuguchi
Apr 30, 2017·Chemical Science·Guo-Bo LiChristopher J Schofield
Jul 1, 2017·Journal of Chemical Information and Modeling·Guo-Bo LiSheng-Yong Yang
Jul 8, 2017·The Journal of Biological Chemistry·Maria BakouAphrodite Kapurniotu
Sep 16, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Vivitri PrasastyEnade Istyastono

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Citations

May 1, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Enade P IstyastonoSudi Mungkasi

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