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AQUA-DUCT: a ligands tracking tool

2017; Oxford University Press; Volume: 33; Issue: 13 Linguagem: Inglês

10.1093/bioinformatics/btx125

1367-4811

Tomasz Magdziarz, Karolina Mitusińska, Sandra Gołdowska, Alicja Płuciennik, Michał Stolarczyk, Magdalena Ługowska, Artur Góra,

Spectroscopy and Quantum Chemical Studies

Abstract Motivation The identification and tracking of molecules which enter active site cavity requires screening the positions of thousands of single molecules along several thousand molecular dynamic steps. To fill the existing gap between tools searching for tunnels and pathways and advanced tools employed for accelerated water flux investigations, we have developed AQUA-DUCT. Results AQUA-DUCT is an easy-to-use tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein. It can be used for any type of molecules, e.g. water, oxygen, carbon dioxide, organic solvents, ions. Availability and Implementation Linux, Windows, macOS, OpenBSD, http://www.aquaduct.pl. Supplementary information Supplementary data are available at Bioinformatics online.