Publication describing new version of the AQUA-DUCT tool is available in Advance article section 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…
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.
AQUA-DUCT was cited in article on “Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization” See more here.
The AQUA-DUCT software was used for loop functionality analysis.
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…
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…
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.
The AQUA-DUCT was used to investigate internal architecture of Soluanum Tuberosum Epoxide Hydrolase. See more in Biomolecules 2018, 8(4) 143.
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…
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
AQUA-DUCT software will be presented in September during seventeenth edition of the European Conference on Computational Biology in Athens in Greece. It will be presented during ECCB 2018 Application Track part of he conference. The aim of the track is to give a voice to those who apply computational biology in industry, clinics, governmental organizations, and other fields beyond…
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:…
The AQUA-DUCT presentation was selected for speed talk and will be presented during 43rd FEBS congress held in Praha, Czech Republick, 2-7 July 2018.
AQUA-DUCT software and its results will be presented during Artificial Water Channels Faraday Discussion organised by Royal Society of Chemistry. Event is organised in Glasgow UK 25-27.062018.
AQUA-DUCT software and its results will be presented during Enzymes, biocatalysis and chemical biology: The new frontiers organised by EMBO in Pavia, Italy 9-12 09 2018.
The AQUA-DUCT workshop took place during 10th Edition of International Conference on Structural Biology 15-16 March, Barcelona
New version of AQUA-DUCT is available (Release 0.5.9) Rewritten module for MD data access. Sandwich mode added. Coordinates can be stored in cache directory, in memory or generated on demand. Support for long trajectories. Passing through paths are supported. Improvements in visualization script. Coordinates of residues are calculated as center of geometry. Recommended MDAnalysis…
New version of AQUA-DUCT is available (Release 0.4.14) Uses newest MDAnalysis (0.16.2). Steady improvement of documentation (including API). Names of traced molecules are returned in the result file and tables are split appropriately. Tables in the result file are split in regard to Object and Passing paths. Passing through paths are being introduced, WIP. Additional…