How to cite:

NEW VERSION (from 1.0.0)

T. Magdziarz, K. Mitusińska, M. Bzówka, A. Raczyńska, A. Stańczak, M. Banas, W. Bagrowska, A. Góra, AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective, Bioinformatics, , btz946, https://doi.org/10.1093/bioinformatics/btz946

ABSTRACT
Motivation: Tunnels, pores, channels, pockets and cavities contribute to proteins architecture and performance. However, analysis and characteristics of transportation pathways and internal binding cavities are performed separately. We aimed to provide universal tool for analysis of proteins integral interior with access to detailed information on the ligands transportation phenomena and binding preferences.
Results: AQUA-DUCT version 1.0 is a comprehensive method for macromolecules analysis from the intramolecular voids perspective using small ligands as a molecular probes. This version gives insight into several properties of macromolecules and facilitates protein engineering and drug design by the combination of the tracking and local mapping approach to small ligands.
Supplementary information: Supplementary data are available at Bioinformatics online.


OLD VERSION (before 1.0.0)

T. Magdziarz, K. Mitusińska, S. Gołdowska, A. Płuciennik, M. Stolarczyk, M .Ługowska and A. Góra; AQUA-DUCT a ligands tracking tool. Bioinformatics (2017) 33 (13): 2045-2046. DOI: 10.1093/bioinformatics/btx125 ARTICLE or PROOF VERSIONOpen Access

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.

Platform and Availability: Linux, Windows, macOS, OpenBSD, http://www.aquaduct.pl

Contact: a.gora@tunnelinggroup.plinfo@aquaduct.pl

Supplementary information Open Access

AQUA-DUCT DOCUMENTATION_v0.5.9Open Access   OLD VERSION – for new version visit DOCUMENTATION section.

The available copy of paper is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Bioinformatics (2017) 33 (13): 2045-2046. is available online at: https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx125/3059930/AQUA-DUCT-a-ligands-tracking-tool?redirectedFrom=fulltext DOI: 10.1093/bioinformatics/btx125.

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