AQUA-DUCT in IJMS Review

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.

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

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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

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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     

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The AQUA-DUCT was used to study ion permeability through claudin-2 dimer interface, the work of Flaviyan Jerome Irudayanathan and co-workers was published in J. Phys. Chem. B        

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The AQUA-DUCT software was used to analyse water access into D-amino acid oxidase (DAAO). The results were published recently in PLOS ONE journal. 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:

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AQUA-DUCT was cited in VCBM 17: Eurographics Workshop on Visual Computing for Biology and Medicine in article Watergate: Visual Exploration of Water Trajectories in Protein Dynamics by Viktor Vad and co-workers.