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…
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:…