MicroMiner

MicroMiner searches protein structure databases for local 3D micro-environments to identify single-residue substitutions and analyze structural changes upon mutation.

Key Features:

• Residue-defined local 3D micro-environment search: Searches local sites in protein structure databases using residue-defined local 3D micro-environments based on the SIENA methodology.
• Structural mutation analysis: Identifies single-residue substitutions by searching protein residue environments with local sequence and structural similarity.
• Database coverage: Enables searching the entire PDB, in-house structure collections, or subsets of the AlphaFold Database.
• Interface analysis: Supports analysis of single domains, protein-protein interfaces, and protein-ligand interfaces.
• Mutation effect annotation: Annotates experimentally measured mutation effect data sets, such as Delta Delta G measurements, with extracted structure pairs to combine mutation effect measurements with structural changes upon mutation.
• Structure-based drug design integration: Bridges mutation analysis with structure-based drug design tools.
• Large-scale pair extraction: Extracted over 255 million amino acid pairs in protein structures from the PDB for single chains and over 45 million pairs for protein-protein interfaces.

Scientific Applications:

• Structural mutation analysis: Explores the mutation landscape of proteins with experimental or predicted structures when wild-type and mutant experimental structures are unavailable.
• Mutation effect interpretation: Combines experimentally measured mutation effects with structural changes upon mutation to understand the structural basis of mutation impacts.
• Protein interface characterization: Analyzes structural mutations at protein-protein and protein-ligand interfaces.
• Structure-based drug design: Connects mutation analysis results to structure-based drug design workflows.

Methodology:

MicroMiner implements residue-defined local 3D micro-environment search based on the SIENA methodology.