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

AQUA-DUCT was applied to study deubiquitinylases

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.

AQUA-DUCT – Release 1.0.0 is available

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


25th of July, AQUA-DUCT will be presented during lecture in Heidelberg Institute for Theoretical Studies. It will be first presentation of new version of AQUA-DUCT.

New Citation

AQUA-DUCT was cited in article on “Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization” See more here.  


The picture of the results of AQUA-DUCT analysis were selected for recent cover of Bioinformatic issues! SEE MORE COVER story: Cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. Using a 3DM-based bioinformatics approach, a pair of amino acids in the periphery of the PfPGI structure was found to

New citation

The AQUA-DUCT was used to study Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase. Recent paper was published in  Biomolecules 2019, 9(6), 212. The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosuscatalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of

New citation

AQUA-DUCT was cited in recent review published in Biotechnology Advances: “Engineering enzyme access tunnels” Piia Kokkonen, David Bednar, Gaspar Pinto, Zbynek Prokop, and Jiri Damborsky. ARTICLE     


AQUA-DUCT will be presented during School on molecular computational biochemistry  that will take on 11-14 March place in the Jerzy Haber Institute of Catalysis and Surface Chemistry in Kraków. 


AQUA-DUCT was presented on FEBS congress during speed-talk session Biochemistry and Signaling held on Monday, July 9, 2018. To facilitate analysis of the behaviour of water (and if necessary other solvent molecules or ligands) we have developed AQUA-DUCT. Here we would like to provide an example of its usage for analysis of water transportation in selected enzymes (epoxide hydrolases