VADAR

VADAR evaluates protein structures by calculating volumetric, surface, dihedral angle, and related structural parameters to quantify residue-level and whole-protein quality.

Key Features:

• Input formats: Accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input.
• Extensive parameter analysis: Calculates over 30 structural parameters, including excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure elements, hydrogen bonding partners and their energies, steric quality, solvation free energy, and local and overall fold quality.
• Per-residue and global metrics: Provides residue-level and whole-protein evaluations for identifying local anomalies and global fold assessments.
• Reporting: Produces graphical representations and detailed reports summarizing computed structural parameters and quality metrics.
• Issue identification: Flags residue-specific and general structural problems based on evaluated parameters.

Scientific Applications:

• Structural validation: Identifies general and residue-specific problems to aid validation of newly solved protein structures.
• Quality assessment: Assesses local and overall fold quality to evaluate accuracy of structural models.
• Protein engineering and drug discovery support: Provides structural metrics useful for applications in drug design, enzyme engineering, and interpreting protein function.

Methodology:

Computes >30 structural parameters from PDB coordinates—including excluded volume, accessible surface area, dihedral angles, secondary structure, hydrogen bond partners and energies, steric quality, and solvation free energy—and evaluates these metrics to assess residue-level and global fold quality, producing graphical and textual reports.