GeoMine
GeoMine is a tool for the automated mining of protein–ligand binding sites. It enables users to define custom queries and search large collections of protein–ligand complexes and binding pockets for specific spatial interaction patterns. GeoMine supports ligand-based radius pockets as well as predicted pockets generated with DoGSite3 and provides matched binding-site superpositions together with geometric statistics.
Key benefits
Automated search for spatial patterns in protein–ligand binding sites
Custom query design for specific interaction geometries
Searches large, regularly updated collections of protein structures and pockets
Supports ligand-based and DoGSite3-predicted binding pockets
Available through a graphical interface and REST service
Provides structural superpositions and statistics on distances, angles, and matching points
Applications
Identification of recurring interaction patterns in protein binding sites
Comparison of geometrically similar binding pockets
Analysis of conserved ligand-binding arrangements
Discovery of structurally related binding sites across different proteins
Support for structure-based drug discovery and ligand design
Generation of reference sets for binding-site classification and validation
Intended use
GeoMine is intended for structural biologists, medicinal chemists, computational chemists, and bioinformaticians working with protein–ligand complexes and binding-site geometries. It is particularly suited for users who want to search large structural datasets for custom spatial interaction patterns and compare matched binding sites in detail.
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