GeoMine

GeoMine searches user-defined three-dimensional queries within protein-ligand interfaces to identify geometrically matching patterns across Protein Data Bank (PDB) complexes.

Key Features:

• Versatile Query Generation: Supports textual, numerical, and geometrical search modes and constructs queries from a 3D representation of a starting structure with selectable atoms, bonds, and interactions.
• Geometric Variability Control: Provides explicit control over geometric tolerance in queries while ensuring deterministic and precise matching of spatial patterns.
• Deterministic Precision: Produces precise, reproducible search results for highly selective queries across protein-ligand complexes.
• Scalability and Speed: Processes reasonably selective queries across the entire set of protein-ligand complexes in the PDB within minutes.
• ProteinsPlus Integration: Integrated into the ProteinsPlus suite for structure-based modeling workflows.

Scientific Applications:

• Off-target and Side-effect Analysis: Enables identification of potential off-target protein-ligand interactions and geometrically similar binding-site motifs that may contribute to drug side effects.

Methodology:

Performs searches of Protein Data Bank (PDB) structural data using user-defined three-dimensional queries with configurable geometric variability.