admin – Page 2 – AQUA-DUCT by Tunneling Group.

New citation

May 31, 2019adminCitation

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…

New citation

Apr 23, 2019adminCitation

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 event

Mar 10, 2019adminEvent

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.

New citation

Nov 15, 2018adminCitation, News

The AQUA-DUCT was used to investigate internal architecture of Soluanum Tuberosum Epoxide Hydrolase. See more in Biomolecules 2018, 8(4) 143.

AQUA-DUCT event

Jul 29, 2018adminEvent

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…

New citation

Jun 26, 2018adminCitation, News

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

Jun 15, 2018adminEvent, News

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…

New citation

Jun 15, 2018adminCitation, News

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

May 15, 2018adminEvent, News

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

May 5, 2018adminEvent, News

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

Apr 23, 2018adminEvent, News

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

Mar 16, 2018adminEvent, News

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

Mar 12, 2018adminNew version, News

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

Nov 20, 2017adminNew version, News

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…

New citation

Sep 25, 2017adminCitation

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.

Tips and tricks – clustering – new version.

Jul 25, 2017adminNews

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

Jul 17, 2017adminNew version, News

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

Jun 26, 2017adminNew version, News

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

Jun 23, 2017adminNews

AQUA-DUCT publication was published in Volume 33, Issue 13 of Bioinformatics journal – AQUA-DUCT a ligand tracking tool

Tips and tricks – clustering.

May 18, 2017adminNews

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.