Overview

vBROOD is the graphical interface that ships with BROOD. It gives access to all the command-line features as well as some GUI-only features, such as query and filter editing, and placing constraint and color atoms.

vBROOD allows users to interactively design filters to limit the scope of the database search or produce results with properties in an expected range. This can improve both the run-time performance and the quality of the output structures.

Upon completion, BROOD clusters the result molecules. vBROOD presents the cluster heads for viewing; the full clusters can be explored in VIDA (see Viewing Results in VIDA).

Most BROOD options can be changed from within vBROOD. vBROOD can easily run BROOD in multiprocessor mode. vBROOD cannot, however, run BROOD across a cluster.

Task Screen

The vBROOD task screen

vBROOD offers five tasks to help run BROOD:

  • Build and Run: Create a query and immediately start a BROOD run.

  • Build a New Query: Create and edit a query to save and later send to a BROOD run.

  • Run BROOD: Run BROOD with a previously created filter and query.

  • Filtering: Create filters for BROOD and post-filter hitlists from previous runs.

  • View Results: Browse results and launch the BROOD interface in VIDA.