BROOD 3.0.0

July 2015

This is a significant release of BROOD. It primarily to add user-requested features and to fix user-reported bugs. It includes important improvements in all four programs included in the BROOD suite as well as numerous bug fixes. This release of BROOD also include support for several new Linux platforms as well as support for MPI multi-processing on Windows.

Platform Support

  • Added support for RedHat 6, 7, Ubuntu 14, OSX 10.7, 10.8, 10.9

  • Dropped support for RedHat 5 32 bit and OSX 10.6

  • Added MPI support for Windows

  • This will be the last release for SuSe 11


  • Added auto-suggestion of fragments for replacement in query

  • Reduced arbitrary strict stereo in query build

  • Streamlined query building, searching and results view

  • Improved cluster handling in hitlist filtering

  • Added 2D alignment of results viewing

  • Added upper and lower bound to filter properties

Results Viewer

  • Annotation of hitlist molecules with color atoms

  • Improved cluster navigation

  • Cleaned up cluster naming and manipulation

  • Improved viewer widget layout

  • Improved visibility of keyboard shortcuts and navigation


  • Substantial improvement to the calculation of local strain

  • Improved elimination of over-strained analogs

  • Added the ability to suppress protein output in hitlists

  • Added the ability to annotate results with similar molecules from a user collection

  • Added protein selectivity

  • Fixed problems with property flag

  • Fixed bug in frequency data

  • Added upper and lower bound to filter properties


  • Added the ability to pull fragment conformations from user-supplied structure database

  • Added new fragment database derived from ChEMBL [Bento-2014]

  • Mapping of top 5 source molecules onto each fragment

  • Added enumeration of stereochemistry to CHOMP

  • Fixed inconsistency between single-processor and MPI duplicate removal


  • Improved user interface with clearer output and verbose output

  • Added support for duplicate recognition and removal

  • Added ability to overwrite existing databases if necessary