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29Jul/18

AQUA-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 and cytochrome p450). An advanced clustering and pathway trimming methods were used for trajectory grouping. An immediate and easy access to statistical data combined with visualisation of water entry clusters and each water molecule trajectory enable detection of transportation pathways, residues controlling access to active sites, preferable flow direction and other features not accessible by other tools.

 

15Jun/18

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 academia. With advanced science and technology finding its ways everywhere, many clinicians, analysts, data scientists have more and more to share with scientists in academia. A plethora of scientists currently works outside of academia, and may not be interested or are sometimes restricted to publish, thus making themselves and their work invisible to the academic community. This track is a platform for presenting such applications, some of which may well be untraditional or otherwise not often heard at academic conferences.
15Jun/18

New 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: 10.1371/journal.pone.0198990 ARTICLEOpen Access

Trajectories of selected water molecules which has entered active site during MD simulations calculated by AQUA-DUCT. Each figure presents trajectory of single water molecule divided into 4 parts: inside active site cavity (green line), from surface to the active site cavity (red lines), from active site cavity to the surface (blue lines) and that parts when water has left active site and travel back again due to geometrical constrains (yellow line), the number corresponds to raw path numbering by AQUA-DUCT.
12Mar/18

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 is set to >=0.16 and <0.17. Version 0.17 is supported but not recommended.
  • Bug fixes and code cleanup.

For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.

 

20Nov/17

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 tables in the result file.
  • CRD is enabled as topology/trajectory format.
  • Traced residues are identified by resindices instead of resids; this allows to use weak topologies such as PDB.
  • Removed roman dependency.
  • In addition to histograms approximate (ConvexHull approximation) areas and volumes of the scope and object can be calculated.
  • Bug fixes and reliability fixes.

For more specific information on new functionalities see changelog at http://pythonhosted.org/aquaduct/.

25Jul/17

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.

18May/17

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.