AQUA-DUCT is a new tool facilitating analysis of the flow of solvent molecules in molecular dynamic simulations.

AQUA-DUCT allows extraction, analysis and visualization of the behaviour of solvent molecules during the entire simulation. Such analysis can be useful for the analysis of the enzymes with a buried active site, connected with surrounding solvent by tunnels. The water flow can be controlled by molecular properties of amino acids constituting tunnels or in more sophisticated enzymes by gates controlling the opening and closing of the access pathways. For more details please read our articles (AQβ, AQ1.0) or visit dedicated web page.

An example of AQUA-DUCT results. Approximated trajectories of all water molecules detected in active site cavity during MD simulations of M. musculus epoxide hydrolase.

How to cite: 1. 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 2019, 1–3. https://doi.org/10.1093/bioinformatics/btz946 2. T. Magdziarz et al., AQUA-DUCT a ligands tracking tool. Bioinformatics 2017 btx125. doi: 10.1093/bioinformatics/btx125