BoBER

BoBER provides a database of bioisosteric and scaffold replacements mined from the Protein Data Bank (PDB) to support exploration and application of bioisosterism and scaffold hopping in drug design.

Key Features:

• Bioisosterism and Scaffold Hopping: Proposes fragment-level bioisosteric substitutions and scaffold-level replacements while preserving pharmacophoric elements.
• Fragment Replacement Database: Contains potential replacements for biologically active compound fragments derived from structural data.
• PDB-Derived Data Mining: Database populated by mining the entire Protein Data Bank (PDB) to generate replacement candidates from PDB entries.
• Replacement Objectives: Provides replacement candidates aimed at enhancing activity, reducing toxicity, altering bioavailability, or diversifying chemical scaffold space.

Scientific Applications:

• Drug Design and Lead Optimization: Supports exploration and application of bioisosteric and scaffold hopping concepts to optimize hit and lead compounds in medicinal chemistry.
• MurF Inhibitor Case Study: Applied to an existing MurF inhibitor to identify novel bioisosteric or scaffold replacements.

Methodology:

Database populated by mining the Protein Data Bank (PDB).