BMaps

BMaps facilitates fragment-based drug design by using thermodynamically rigorous Monte Carlo simulations and precomputed fragment maps to identify and rank fragment binding orientations on protein structures.

Key Features:

• Extensive protein repository: Contains over 550 protein structures with precomputed fragment maps, druggable hot spots, and high-quality water maps.
• Thermodynamically rigorous Monte Carlo simulations: Uses Monte Carlo sampling to model fragment binding thermodynamics.
• Automated fragment search and ranking: Searches multigigabyte datasets, identifies bondable orientations, and ranks fragments using a binding-free energy metric.
• Structure database integration: Supports user-provided protein structures and structures from the Protein Data Bank (PDB) and AlphaFold DB.
• Combination with conventional computational tools: Integrates docking and energy minimization with fragment-based design workflows.

Scientific Applications:

• Preclinical drug discovery: Supports the design and prioritization of small molecules in preclinical programs.
• Fragment-based lead identification and optimization: Enables exploration of fragment binding data to guide assembly and optimization of drug candidates.
• Binding site characterization: Identifies druggable hot spots and maps water networks on protein structures.

Methodology:

Thermodynamically rigorous Monte Carlo simulations on precomputed fragment maps, automated fragment search of multigigabyte datasets with identification of bondable orientations, ranking by a binding-free energy metric, and integration of docking and energy minimization.