PROPORES

PROPORES identifies and analyzes pockets, cavities, tunnels, and pores in protein structures and assesses their accessibility and connectivity to support studies of ligand-binding pockets and molecular movement through channels.

Key Features:

• Systematic Identification: Employs computational algorithms to identify pockets, cavities, tunnels, and pores within protein structures.
• Flexibility Analysis: Simulates rotation of side chains of gating residues to assess structural adaptability and potential access to occluded ligand-binding pockets or blocked channels.
• Connection Identification: Detects connections between separate pores within a single protein and links internal pores with the surrounding protein matrix to reveal potential molecular pathways.

Scientific Applications:

• Aquaporin: Applied to aquaporin structures to identify and analyze structural features and aid in elucidating protein mechanisms.
• Tryptophan synthase: Applied to tryptophan synthase structures to identify and analyze structural features and aid in elucidating protein mechanisms.
• Leucine transporter: Applied to the leucine transporter to identify and analyze structural features and aid in elucidating protein mechanisms.
• Acetylcholinesterase: Applied to acetylcholinesterase structures to identify and analyze structural features and aid in elucidating protein mechanisms.

Methodology:

Computational analysis integrates structural data with simulations of side chain movements, including rotation of gating-residue side chains, to assess accessibility and flexibility not fully captured in static X-ray crystallography structures.