AQUA-DUCT against COVID-19
We have applied AQUA-DUCT to investigate and compare SARS and COVID-19 Mpro. Check on BioRxiv
AQUA-DUCT 1.0 PUBLISHED IN “BIOINFORMATICS”
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.
AQUA-DUCT is on the COVER
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…
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The AQUA-DUCT was used to investigate internal architecture of Soluanum Tuberosum Epoxide Hydrolase. See more in Biomolecules 2018, 8(4) 143.
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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
AQUA-DUCT event
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…
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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:…
AQUA-DUCT event
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 event
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 event
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.
AQUA-DUCT workshop
The AQUA-DUCT workshop took place during 10th Edition of International Conference on Structural Biology 15-16 March, Barcelona
AQUA-DUCT – Release 0.5.9 is available
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…
AQUA-DUCT – Release 0.4.14 is available
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…
Tips and tricks – clustering – new version.
Check out the updated clustering tips and tricks in the Tutorials section Adjusting method of clustering This section will show you how your results can vary from chosen method of clustering ……. For a new PDF file version of the tutorial visit the Download section.
AQUA-DUCT – Release 0.3.7 is available
New version of AQUA-DUCT is available (Release 0.3.7) Enable XTC trajectory format. Reliability fix in progress bar display. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
AQUA-DUCT – Release 0.3.6 is available
New version of AQUA-DUCT is available (Release 0.3.6) AQ can be run for given part of trajectory. Fixed bug in passing options to Barber clusterization method. Recursive threshold can be defined as range; no disjoint ranges are supported. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
AQUA-DUCT publication was published
AQUA-DUCT publication was published in Volume 33, Issue 13 of Bioinformatics journal – AQUA-DUCT a ligand tracking tool
Tips and tricks – clustering.
Check out the clustering tips and tricks in the Tutorials section Adjusting method of clustering This section will show you how your results can vary from chosen method of clustering ……. For a PDF file version of the tutorial visit the Download section.
AQUA-DUCT – Release 0.3.5 is available
New version of AQUA-DUCT is available (Release 0.3.5) As for now, the only supported version of MDAnalysis is 0.15. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.
AQUA-DUCT – Release 0.3.4 is available
New version of AQUA-DUCT is available (Release 0.3.4) Fixed bug in progress bar updating method causing critical error in some specific circumstances. For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.