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.
- 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.