KINARI-Web

KINARI-Web performs rigidity analysis and visual exploration of rigidity properties in protein structures to assess mechanical stability and flexibility.

Key Features:

• Rigidity Analysis: Performs detailed rigidity analysis on protein structures to identify rigid and flexible regions.
• Data Pre-processing Tools: Supports selection of relevant chains from PDB files, addition of hydrogen atoms, and identification of stabilizing interactions.
• Customizable Analysis Options: Enables selection or removal of specific chains, residues, or atoms, addition or elimination of stabilizing constraints, and specification of how chemical interactions are modeled in the analysis.
• Visualization: Incorporates a Jmol-based visualizer to inspect and interpret calculated rigidity properties.

Scientific Applications:

• Protein dynamics and stability: Analyzes rigidity to provide insights into protein mechanical stability and flexibility under physiological conditions.
• Mutation and interaction analysis: Evaluates how mutations or molecular interactions affect local and global protein rigidity.
• Drug design: Informs drug design by characterizing target protein flexibility relevant to ligand binding and therapeutic development.

Methodology:

Uses computational modeling and visualization techniques to assess rigidity properties, with preprocessing steps that include chain selection from PDB files, addition of hydrogen atoms, and identification of stabilizing interactions; analysis parameters and stabilizing constraints can be customized and results are interpreted with a Jmol-based visualizer.