MOLE PyMOL plugin

MOLE PyMOL plugin extends MOLE 2.0 to analyze and visualize molecular channels and pores in proteins and nucleic acids.

Key Features:

• PyMOL integration: Integrates with PyMOL to visualize and analyze channels and pores in biomacromolecules.
• Automatic Detection: Provides extended options to automatically detect starting points of channels for channel identification.
• Channel Filtering: Implements filtering mechanisms to select biologically relevant channels from identified candidates.
• Physicochemical Property Estimation: Estimates hydropathy, hydrophobicity, polarity, charge, and mutability of channels.

Scientific Applications:

• Molecular recognition: Enables analysis of channel properties to investigate molecular recognition and substrate specificity.
• Enzyme substrate specificity: Assesses channel physicochemical features to correlate with enzyme substrate access and specificity.
• Structure–function analysis: Facilitates analysis of structural and functional aspects of molecular channels and pores across biomacromolecules.
• Drug design and enzyme mechanisms: Provides physicochemical profiles of channels to support hypotheses in drug design and enzyme mechanism studies.
• Protein–nucleic acid interactions: Supports exploration of channels in protein–nucleic acid complexes by characterizing their physicochemical properties.

Methodology:

Developed as part of MOLE 2.0; uses algorithms benchmarked against other software tools and analyzes X-ray structures to assess variability in channel physicochemical properties across biomacromolecules, including cytochrome P450 superfamily members.