RECORDED WEBINAR AVAILABLE ON-LINE
Our webinar on MOLECULAR DYNAMICS SIMULATIONS ANALYSIS WITH MOLECULAR PROBES was held twice on 23rd of September 2020. Now you can watch the recorded video published on our YouTube channel.
0
0AQUA-DUCT was used to study inhibitors of the 5-LOX – a non-heme iron containing dioxygease.
AQUA-DUCT was used to study inhibitors of the 5-LOX – a non-heme iron containing dioxygease. The study were published in the Journal of Biomolecular Structure and Dynamics.
0WEBINAR – MOLECULAR DYNAMICS SIMULATIONS ANALYSIS WITH MOLECULAR PROBES
The AQUA-DUCT webinar was held on 23rd September 2020. Thank you for participation.
0AQUA-DUCT in IJMS Review
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
0AQUA-DUCT was applied to study deubiquitinylases
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.SUMMER SCHOOL POSTPONE
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.
0AQUA-DUCT against COVID-19
We have applied AQUA-DUCT to investigate and compare SARS and COVID-19 Mpro. Check on BioRxiv
0AQUA-DUCT applied for water intake study
Nice work has been just published in Journal of Physical Chemistry B. Thank you for using our software.0AQUA-DUCT in CSBJ Review
“Applications of water molecules for analysis of macromolecule properties” provides more examples how the water molecule can/should be considered in your study.
0AQUA-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.
0AQUA-DUCT – Release 1.0.0 is available
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…
0New Citation
AQUA-DUCT was cited in article on “Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization” See more here. 
0
0AQUA-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…
0New citation
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…
0New citation
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 
0AQUA-DUCT event
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. 
0New citation
The AQUA-DUCT was used to investigate internal architecture of Soluanum Tuberosum Epoxide Hydrolase. See more in Biomolecules 2018, 8(4) 143.
0AQUA-DUCT event
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…
0New citation
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 
0AQUA-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…
0New citation
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:…
0AQUA-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.
0AQUA-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.
0AQUA-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.
0AQUA-DUCT workshop
The AQUA-DUCT workshop took place during 10th Edition of International Conference on Structural Biology 15-16 March, Barcelona0AQUA-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…0AQUA-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…
0New citation
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.
0Tips 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.0AQUA-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/.0AQUA-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/. 
0AQUA-DUCT publication was published
AQUA-DUCT publication was published in Volume 33, Issue 13 of Bioinformatics journal – AQUA-DUCT a ligand tracking tool0Tips 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.0AQUA-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/.0AQUA-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/.0AQUA-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/.0AQUA-DUCT publication in Advance articles section “Bioinformatics”
New publication describing AQUA-DUCT tool is available in Advance article section in “Bioinformatics”: AQUA-DUCT a ligand tracking tool
0AQUA-DUCT is launched
Our tool AQUA-DUCT is officially launched (Release 0.3.2) Major improvement: new auto_barber based clustering method. Clusterization history displayed as simple ascii tree. AutoBarber min and max cut level options added. Barber moved to separate module. Fixed bug in visualization script; if no molecule is kept do not set style and color. New publication…
0
0AQUA-DUCT was used to study inhibitors of the 5-LOX – a non-heme iron containing dioxygease.
AQUA-DUCT was used to study inhibitors of the 5-LOX – a non-heme iron containing dioxygease. The study were published in the Journal of Biomolecular Structure and Dynamics.
0WEBINAR – MOLECULAR DYNAMICS SIMULATIONS ANALYSIS WITH MOLECULAR PROBES
The AQUA-DUCT webinar was held on 23rd September 2020. Thank you for participation.
0AQUA-DUCT in IJMS Review
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
0AQUA-DUCT was applied to study deubiquitinylases
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.
SUMMER SCHOOL POSTPONE
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.
0AQUA-DUCT against COVID-19
We have applied AQUA-DUCT to investigate and compare SARS and COVID-19 Mpro. Check on BioRxiv
0AQUA-DUCT applied for water intake study
Nice work has been just published in Journal of Physical Chemistry B. Thank you for using our software.
0AQUA-DUCT in CSBJ Review
“Applications of water molecules for analysis of macromolecule properties” provides more examples how the water molecule can/should be considered in your study.
0AQUA-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.
0AQUA-DUCT – Release 1.0.0 is available
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…
0New Citation
AQUA-DUCT was cited in article on “Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization” See more here.
0
0AQUA-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…
0New citation
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…
0New citation
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
0AQUA-DUCT event
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.
0New citation
The AQUA-DUCT was used to investigate internal architecture of Soluanum Tuberosum Epoxide Hydrolase. See more in Biomolecules 2018, 8(4) 143.
0AQUA-DUCT event
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…
0New citation
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
0AQUA-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…
0New citation
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:…
0AQUA-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.
0AQUA-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.
0AQUA-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.
0AQUA-DUCT workshop
The AQUA-DUCT workshop took place during 10th Edition of International Conference on Structural Biology 15-16 March, Barcelona
0AQUA-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…
0AQUA-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…
0New citation
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.
0Tips 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.
0AQUA-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/.
0AQUA-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/.
0AQUA-DUCT publication was published
AQUA-DUCT publication was published in Volume 33, Issue 13 of Bioinformatics journal – AQUA-DUCT a ligand tracking tool
0Tips 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.
0AQUA-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/.
0AQUA-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/.
0AQUA-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/.
0AQUA-DUCT publication in Advance articles section “Bioinformatics”
New publication describing AQUA-DUCT tool is available in Advance article section in “Bioinformatics”: AQUA-DUCT a ligand tracking tool
0AQUA-DUCT is launched
Our tool AQUA-DUCT is officially launched (Release 0.3.2) Major improvement: new auto_barber based clustering method. Clusterization history displayed as simple ascii tree. AutoBarber min and max cut level options added. Barber moved to separate module. Fixed bug in visualization script; if no molecule is kept do not set style and color. New publication…