Join our upcoming webinar on 24 March 2026 at 15:00 CET to explore AQUA-DUCT! Workshop will introduce technical background and practical use of solvent tracking to investigate internal pathways, identify regions where small molecules become trapped and understand how water behavior supports enzymatic mechanism studies, protein engineering and drug design. More information and registration: here
AQUA-DUCT was used to track gas molecules inside hydrogenases and identify their unbinding pathways, providing reference pathway assignments for clustering and machine learning model training. Solvent and ligand pathway analysis enabled classification of transport routes and analysis of MD trajectories. More information here
AQUA_DUCT was used to analyze water accessibility to active site of Acetylcholinesterase, confirming presence and relative usage of main tunnel and pathway. Solvent pathway analysis provides structural and functional insight valuable for inhibitor design and antidote development. Read full article here
AQUA-DUCT was used to track water molecules inside enzyme and identify solvent pathways connecting active site with protein surface. It provides insight into molecular transport and it’s relation to enzyme function. Read full article here
An excellent possibility to get insights how AQUA-DUCT can help with enzymes engineering was presented by Agata one f the AQUA-DUCT developer during poster session and pitch talk at Wageningen.
Next application of the AQUA-DUCT for COVID-19 related proteins. This time the NSP13 helicase of SARS-CoV-2 is studied. Please read more here.
Interesting application of the AQUA-DUCT in complex system. Please check more here.
Our next study on main protease of the SARS-CoV2 is out. This time AQUA-DUCT was used to predict similarities between binding cavities of several proteases. More here.
Our webinar on MOLECULAR DYNAMICS SIMULATIONS ANALYSIS WITH MOLECULAR PROBES was held twice on 23rd of September 2020. Now you can watch the recorded video published on our YouTube channel.
AQUA-DUCT was used to study inhibitors of the 5-LOX – a non-heme iron containing dioxygease. The study were published in the Journal of Biomolecular Structure and Dynamics.
The AQUA-DUCT webinar was held on 23rd September 2020. Thank you for participation.
Next study using AQUA-DUCT in studies about ebselen binding activity to SARS-CoV-2 main protease. More here.
The AQUA-DUCT software was describe in details in recent review: Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering, Int. J. Mol. Sci.2020, 21(8), 2713. More you can find here
An interesting study has been just published in Journal of Biological Chemistry aiming to investigate differences between OTUB1 and OTUB2 that may be relevant for the selective design of ovarian tumor domain deubiquitinylating cysteine proteases inhibitors. We are happy that our software could help to find significant differences. More details here.
The SUMMER SCHOOL OF MOLECULAR DYNAMIC SIMULATIONS ANALYSIS WITH MOLECULAR PROBES is postpone due to COVID-19 pandemic. We will keep you updated. We are planning to set new deadlines and schedules for the event. Preliminary, the REGISTRATION deadline is set on 1.07.2020 and the SUMMER SCHOOL will take place in October.
We have applied AQUA-DUCT to investigate and compare SARS and COVID-19 Mpro. Check on BioRxiv
Nice work has been just published in Journal of Physical Chemistry B. Thank you for using our software.
“Applications of water molecules for analysis of macromolecule properties” provides more examples how the water molecule can/should be considered in your study.
Publication describing new version of the AQUA-DUCT tool is available in “Bioinformatics”. AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective Open access.
New version of AQUA-DUCT is available (Release 1.0.0) The new version of AQUA-DUCT is combining information from small ligands tracking and from small ligands local distribution. New modes of AQUA-DUCT MD data processing: normal, sandwich, time-window and consolidator mode. Pond module for hot-spots identification facilitating protein engineering and drug design, Energy barrier approximation. Graphical User…
