OEDocking 3.4.0

Nov 2019

  • This version of OEDOCKING has been built using OEToolkits 2019.Oct. The previous version was built using OEToolkits 2019.Apr.

New features

  • A new utility application, Spruce4Docking, has been added to properly prepare structures for receptor generation. The output from Spruce4Docking is an OEDesignUnit object serialized to a new OEDU file format. Alternatively, users with access to SPRUCE can take the SPRUCE-generated OEDU files directly and bypass Spruce4Docking.
  • A new utility application, DU2Receptor, has been added that can be used to create a receptor from design units contained in an OEDU file. With the addition of DU2Receptor and Spruce4Docking, previously existing utilities ApoPdb2Receptor, Pdb2Receptor, and ReceptorSetup are no longer required and have been removed from the OEDocking applications suite.
  • POSIT has been rewritten to take advantage of the newly extended corresponding POSIT functionality in the 2019.Oct release of the OEDocking TK. With this update, some of the previous application-specific functionality, including working with multiple receptors, finding the best receptor for a specific ligand, and clash checking, are now directly taken care of by the toolkit functionality. From a performance point of view, POSIT is now more efficient in finding a pose for a ligand when working with multiple receptors. On the downside, there is a slight increase in memory usage and time with use of an increasing number of receptors.
  • The ability to further refine generated poses has been added to POSIT. The optional relaxation allows for greater flexibility of the ligand and parts of the receptor. A new parameter, -relax, has been added that defines if and when this post-pose generation relaxation should be performed.
  • Definition of “clash” and “clash types” have been redefined to be in sync with the definitions in the corresponding functionality in OEDocking TK. The new clash definitions are based on perceived protein-ligand interactions. Accordingly, a new type, hclashes, has been introduced in -allowed_clashes that redefines mildclashes.
  • The -conftest parameter has been removed from all OEDOCKING applications.

Major bug fixes

  • POSIT no longer gives up when the pose generated from the single best receptor produces a clash; it now continues to generate poses with subsequent best receptors until a clash free pose is generated.

Minor bug fixes

  • An issue that caused POSIT to fail to maintain SD Data from the input molecule has been fixed.
  • An issue in HYBRID that caused a single molecule with enumerated nitrogen stereo to be treated as multiple molecules has been fixed.
  • An issue that cuased HYBRID to fail to output undocked molecules to the undocked molecule file for large runs has been fixed.
  • An order-dependent issue in POSIT that affected choosing the best receptor when working with multiple receptors has been fixed. POSIT now gives the same result regardless of the order in which receptors are provided.
  • An issue that caused POSIT to fail to report the correct number of molecules process has been fixed.
  • POSIT no longer crashes when a single atom input molecule is passed.
  • CombineReceptors now recognizes the -prealigned flag.