MolAxis

MolAxis identifies channels within macromolecular structures to locate pathways connecting buried cavities or transmembrane pores and to report geometric and residue-level channel properties.

Key Features:

• Channel identification: Detects channels that connect buried cavities to the external surface and identifies primary transmembrane (TM) channels in proteins.
• Input format support: Processes protein and nucleic acid structures provided in PDB format.
• Channel descriptors: Reports gating residues, the narrowest radius ("bottleneck"), and a comprehensive list of lining residues for each channel.
• Three-dimensional output: Produces a 3D representation of the channel surface.
• Parameter control: Allows adjustment of advanced search parameters to tailor channel detection.

Scientific Applications:

• Membrane transport studies: Characterizes channels relevant to electrolyte and metabolite transport across membranes.
• Enzyme mechanism analysis: Assesses channels that influence enzyme catalysis and substrate specificity.
• Structural-function inference: Supports investigation of macromolecular structures and their functional implications.

Methodology:

Applies advanced computational-geometry techniques to PDB-format protein or nucleic acid structures to identify channels connecting buried cavities to the external surface or the primary channel in transmembrane proteins.