How to cite:

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

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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AQUA-DUCT citations:

2018

F. J. IrudayanathanX. WangN. WangS. R. WillseyI. A. SeddonS. Nangia: Self-Assembly Simulations of Classic Claudins—Insights into the Pore Structure, Selectivity, and Higher Order Complexes, J. Phys. Chem. B, Article ASAP DOI: 10.1021/acs.jpcb.8b03842

K. Subramanian, A. Góra, R. Spruijt, K. Mitusińska, M. Suarez-Diez, V. M. dos Santos, P. J. Schaap: Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS ONE 13(6): e0198990. DOI: 10.1371/journal.pone.0198990 ARTICLEOpen Access

 

2017

V. Vad, J. Byška, A. Jurcík, I. Viola, E. M. Gröller, H. Hauser, S. M. Marques, J. Damborský, B. Kozlíková: Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. Eurographics Workshop on Visual Computing for Biology and Medicine (2017) DOI = {10.2312/vcbm.20171235}