MolProbity

MolProbity validates macromolecular structures by adding and optimizing hydrogen atoms and performing all-atom contact and torsion-angle analyses to detect steric clashes, flipped side chains, covalent-geometry and dihedral-angle outliers in proteins, RNA, complexes, and NMR ensembles.

Key Features:

• Hydrogen Atom Optimization: Adds and optimizes polar and nonpolar hydrogen atoms and corrects 180° flipped sidechains such as Asn, Gln, and His.
• All-Atom Contact Analysis: Performs detailed all-atom contact analysis evaluating hydrogen bonds, van der Waals interactions, and atomic clashes to detect steric problems.
• Covalent Geometry and Dihedral Angle Diagnostics: Assesses covalent geometry and dihedral angles including Ramachandran plots for proteins, ribose-pucker analysis for RNA, and other torsion-angle diagnostics.
• Global and Local Validation Metrics: Computes global and local validation metrics to quantify overall model quality and to localize problematic regions.
• Reporting Formats and Files: Produces numeric scores, lists or charts of local issues, downloadable PDB files, and 3D kinemage graphics for structural inspection.
• Interface Analysis for Complexes: Calculates hydrogen-bonding and van der Waals contacts at molecular interfaces to characterize intermolecular interactions.
• Enhanced RNA and NMR Ensemble Support: Provides specialized analysis functions for RNA structures and NMR ensembles.

Scientific Applications:

• X-ray Crystallography and Structural Determination: Validates atomic models derived from X-ray crystallography and other structural determination methods by identifying local errors such as Ramachandran outliers, flipped branched side chains, and incorrect sugar puckers.
• Interface and Complex Analysis: Characterizes intermolecular hydrogen-bonding and van der Waals contacts at interfaces in molecular complexes.
• RNA and NMR Ensemble Validation: Analyzes RNA conformations including ribose puckers and evaluates NMR ensembles for ensemble-wide validation.
• Model Improvement and Interpretation: Provides validation metrics and detailed diagnostics that support correction of local errors to improve model accuracy and biological interpretation.

Methodology:

Automated addition and optimization of hydrogen atoms, all-atom contact analysis, automated local corrections, covalent-geometry and torsion-angle diagnostics, and generation of numeric and structural validation outputs.