Azahar

Azahar extends PyMOL (version 1.3r1, 2010) to create, visualize, and analyze glycan molecules for structural and conformational studies in glycobiology.

Key Features:

• Glycan construction: Provides tools to create glycan molecular structures within PyMOL.
• Visualization: Introduces three cartoon-like representations specifically tailored for glycans to improve visual interpretation of glycan structures.
• Conformational search: Performs conformational searches using a Monte Carlo method combined with minimization routines to explore 3D glycan conformations.
• Analytical metrics: Calculates radius of gyration, generates Ramachandran plots, and identifies hydrogen bonds for individual glycans and for ensembles or trajectories.
• Implementation: Implemented in Python and integrated as a PyMOL plugin.

Scientific Applications:

• Glycan structural interpretation: Visualize and interpret complex glycan 3D structures using tailored cartoon representations.
• Conformational analysis: Explore energetically favorable glycan conformations and conformational space via Monte Carlo searches with minimization.
• Trajectory and ensemble analysis: Analyze ensembles and molecular dynamics trajectories to quantify radius of gyration and monitor conformational changes.
• Interaction and angle assessment: Assess intramolecular hydrogen bonds and conformational angles using Ramachandran plots to study molecular interactions.

Methodology:

Performs Monte Carlo conformational searches with minimization, computes radius of gyration, generates Ramachandran plots, identifies hydrogen bonds, and implements three cartoon-like glycan representations within a Python-based PyMOL (v1.3r1, 2010) plugin.