BioMe

BioMe analyzes metal-binding sites in protein, RNA, DNA, and other macromolecular chains to produce statistical characterizations of coordination environments, ligand identities, and metal–donor distance distributions.

Key Features:

• Statistical Analysis Capabilities: Calculates statistical properties of metal-binding sites including ligand presence in coordination spheres, coordination number distributions across metal ions, percentages of metal ions coordinated by specified ligand combinations, distributions of monodentate and bidentate bindings for amino acids such as ASP and GLU, and occurrence of binuclear metal centers.
• Coordination Geometry and Descriptive Statistics: Reports coordination geometry classifications and descriptive statistics of metal ion–donor distances to characterize spatial arrangements and bonding characteristics.
• Comprehensive Database Information: Associates each metal ion with Protein Data Bank (PDB) code, structure determination method, types of metal-binding chains (e.g., protein, RNA, DNA), and names and coordinates of bound ligands such as amino acids, nucleotides, and water molecules.
• Graphical and Numerical Presentation: Presents computed statistics in numerical tables and graphical formats for analysis and visualization.

Scientific Applications:

• Structural Biology: Enables analysis of the role and coordination of metals in biological macromolecules for structural interpretation.
• Comparative Bioinformatics: Supports characterization and comparison of metal-binding motifs and coordination patterns across structures, species, or conditions.
• Drug Discovery and Targeting: Informs studies of metalloproteins and metalloenzymes by detailing coordination environments relevant to inhibitor or ligand design.

Methodology:

The underlying database records all contacts within 3 Å of a metal ion observed in asymmetric crystal units.