PSVS

PSVS evaluates protein three-dimensional structures to assess model quality for structures derived from NMR and X-ray crystallography and from homology modeling, providing standardized validation metrics.

Key Features:

• Integration of multiple validation tools: Consolidates analyses from PROCHECK, MolProbity, Verify3D, ProsaII, PDB validation software, and proprietary laboratory tools into combined assessments.
• Standardized quality assessments: Produces constraint analyses, goodness-of-fit statistics between structures and experimental data, and knowledge-based structure quality scores in a standardized format suitable for database integration.
• Global and site-specific measures: Reports both global and site-specific evaluations, with global measures expressed as Z scores calibrated against high-resolution X-ray crystal structures.
• Applicability across methods: Applies to NMR-determined structures, X-ray crystal structures, and homology models for comparative and cross-method quality evaluation.

Scientific Applications:

• Structural genomics quality control: Assessing protein structures generated by the Northeast Structural Genomics Consortium and other international projects over a five-year period.
• Cross-method comparison: Identifying discrepancies between NMR and X-ray crystallographic data and characterizing the "structure quality score gap" between these methods.
• Database curation and integration: Providing standardized validation metrics to support integration of structure quality data into structural databases.

Methodology:

PSVS integrates outputs from multiple structural validation programs and leverages established algorithms and databases to generate standardized quality metrics.