Chemistry Collection 2016 is out now / by Peter Schmidtke

New features

Jointly with our Network Collection, this fresh release brings a few nifty little components allowing our pharmacophore graph (Discngine's reduced graph implementation for Pipeline Pilot) components to efficiently handle molecular conformations and macromolecular structures:

  • Group all conformations of a molecule into a hierarchical data record associated to one pharmacophore graph
  • Calculate average pharmacophore graphs for a set of conformations
  • Use RMSD or distance weighted RMSD values during pharmacophore matching to filter only for interesting conformations
  • Apply rotation & translation matrices obtained during pharmacophore graph superimposition to Pipeline Pilot molecular and macromolecular objects

Example of superimposition of 2 ATP molecules from two crystal structures (1atp & 3k5h) and their structural contexts. Two different protein folds bind the same conformation of ATP.


Improvements

The recursive fragmentation component allows now to consider also hydrogens situated on aromatic cycles during the fragmentation process. This is fully optional and can be easily triggered in the component parameters. When building fragment replacement applications you can use this feature to systematically consider all substitution sites on aromatic rings. 

The component collection is now shipped with regression testing protocols. Thus you can now easily check the installation on your local servers.


Compatibility

The chemistry collection is officially supported for Pipeline Pilot 2016 & 9.x and regression tests have been tailored to these Pipeline Pilot releases.