AQUA-DUCT: a ligands tracking tool

Tomasz Magdziarz; Karolina Mitusinska; Sandra Goldowska; Alicja Pluciennik; Michal Stolarczyk; Magdalena Lugowska; Artur Góra

doi:10.1093/bioinformatics/btx125

AQUA-DUCT: a ligands tracking tool

Bioinformatics. 2017 Jul 1;33(13):2045-2046. doi: 10.1093/bioinformatics/btx125.

Authors

Tomasz Magdziarz¹, Karolina Mitusinska^{1

2}, Sandra Goldowska^{1

2}, Alicja Pluciennik^{1

2}, Michal Stolarczyk^{1

2}, Magdalena Lugowska^{1

2}, Artur Góra¹

Affiliations

¹ Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland.
² Institute of Automatic Control, Silesian University of Technology, Akademicka 16, Gliwice 44-100, Poland.

PMID: 28334160
DOI: 10.1093/bioinformatics/btx125

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 .

Contact: a.gora@tunnelinggroup.pl or info@aquaduct.pl.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Catalytic Domain*
Computational Biology / methods*
Computer Simulation*
Ligands*
Models, Molecular*
Software*

Substances

Ligands