BROOD 2.0.0

April 2010

This is a major rewrite of BROOD including a new database format, faster searching, a much larger database and a graphical interface. The graphical interface greatly simplifies selection of a molecular fragment for replacement and facilitates specification of constraints.

New Features:

  • BROOD now comes with a new graphical application, vBROOD, for setting up searches.

  • Includes specification and graphical editing of color constraints. Pre-defined standard constraints and user-defined constraints are available.

  • New database of more than 3.6 million, common, medicinal fragments.

  • New database format for faster search times.

  • Improved hitlist organization, including a hierarchy based on reduced graphs.

  • Optimized analog molecule overlay.

  • Allows incorporation of a protein structure for clash detection.

  • Graphical interface allows designing of some physical properties.

  • Assessment of synthetic accessibility of generated structures.

  • Implementation of activity belief model for analog molecules.

  • Includes a VIDA extension for ease of exploring results.

  • 1-step database generation, including fragment generation and filtering, charge and property calculation, conformer generation, and buffered database creation.