ValidatorDB

ValidatorDB validates ligands and non-standard residues (molecules with seven or more heavy atoms) in Protein Data Bank (PDB) entries by comparing them against model molecules from the wwPDB Chemical Component Dictionary to detect structural errors, including chirality issues.

Key Features:

• Focus on ligands and non-standard residues: Targets validation of molecules with seven or more heavy atoms within biomacromolecular structures in the PDB.
• Use of wwPDB Chemical Component Dictionary: Employs model molecules from the wwPDB Chemical Component Dictionary as reference standards for validation.
• Chirality error classification: Classifies chirality errors to distinguish severe stereochemical problems from minor inconsistencies.
• Comprehensive validation analyses: Identifies completely erroneous ligands, detects alternate conformations, and confirms complete identity with model molecules.
• Systematic categorization and statistics: Systematically categorizes validation results into distinct categories and performs statistical evaluations of PDB entries.
• Detailed reports and summaries: Produces per-molecule validation reports and summaries for sets sharing the same three-letter code or PDB entry, and for user-defined selections.

Scientific Applications:

• Structural validation: Validation and quality control of ligand and non-standard residue modeling in PDB entries.
• Error identification and correction: Detection of erroneous ligands and alternate conformations that can inform correction of biomolecular structures.
• PDB annotation assessment: Assessment of consistency and correctness of three-letter code annotations across PDB entries.
• Statistical surveys: Generation of statistical evaluations to quantify overall quality and consistency of ligand data in the PDB.

Methodology:

Comparison of PDB molecules to model molecules from the wwPDB Chemical Component Dictionary, classification of chirality errors, systematic categorization of validation results, statistical evaluation, and generation of per-molecule and summary validation reports.