April 2006

This is the first official release of the bioisostere search program BROOD. This release is a significant overhaul of the beta2 release. It includes dramatic feature enhancements, bug fixes and optimizations. Most notable are improvements in the manner in which fragments are ranked and addition of electrostatic similarity. Further, this release has been applied to many bioisostere examples from the medicinal chemistry literature that have helped to refine its performance. Finally, this release makes generation of a custom fragment database much easier.

Release Notes:

  1. Fixed major bug in initial fragment orientation.

  2. Added electrostatic similarity measure

  3. Significantly refined the evaluation functions for ranking bioisosteres.

  4. Added the ability to replace the query fragment with bioisosteric fragments in an initial molecule.

  5. Added separate handling of query analog fragments to avoid filling the hitlists with obvious answers.

  6. Allow user specified partial charges and query conformer.

  7. Allow user defined scaling of the contribution to similarity resulting from the attachment points.

  8. Added the ability to write intermediate hitlists during execution.

  9. Allow user to limit results to ring fragments only.

  10. Refinement of default fragment databases.

  11. Execution speed optimizations.

  12. Addition of two applications for generating a database of molecular fragments.