Vivaldi

Vivaldi analyzes, visualizes, and validates NMR-derived protein structures from the Protein Data Bank (PDB) to assess structure quality and experimental data consistency.

Key Features:

• Interactive Visualization Tools: Provides interactive access to model coordinates and experimental NMR data for exploration of structural models and conformational dynamics.
• Structural Annotations and Model-Validation Information: Supplies structural annotations and validation information for modeled NMR ensembles to evaluate accuracy and reliability.
• Experimental Data Validation: Presents validation data for experimental chemical shifts, residual dipolar couplings, distance constraints, and dihedral angle constraints.
• Validation Scores: Generates validation scores derived from empirical knowledge and existing databases to quantify NMR structure quality.

Scientific Applications:

• Structural Biology Research: Validate and refine protein models using PDB-deposited NMR structures and associated experimental validation metrics.
• Protein Engineering: Inform protein design by providing validated structural data and experimental constraints such as distance and dihedral angle restraints.
• Drug Discovery: Support target characterization and structure-based drug design through validated NMR structural models and experimental restraints.

Methodology:

Integrates and presents complex NMR data, employs advanced visualization techniques to render structural models and experimental data, and bases validation processes on empirical knowledge and existing databases.