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 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

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 – 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 0.3.6 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/.  

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 0.3.3 is available

New version of AQUA-DUCT is available (Release 0.3.3)   AutoBarber default values of maxcut_level and mincut_level changed to True. Improved template configuration file. Number of small improvements in documentation.   For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.