TAP

TAP computes a torsion angle propensity score to validate protein structures by assessing local sequence-to-structure fitness.

Key Features:

• Torsion Angle Propensity Analysis: Measures local sequence-to-structure fitness using torsion angle propensities normalized against global minimum and maximum values.
• Energy Normalization Procedure: Applies a novel energy normalization procedure that enhances the ability to identify optimal experimental structures.
• Improved Accuracy: Outperforms existing validation methods when evaluated against experimental quality parameters on the full Protein Data Bank (PDB) and a subset of obsolete PDB structures.
• Selective Thresholds: Establishes TAP thresholds that recognize over 90% of top-quality experimental structures without requiring additional experimental data.

Scientific Applications:

• Structural biology: Validating experimentally determined protein structures and distinguishing high-quality models from those with potential errors.
• Protein modeling and therapeutic design: Supporting model quality assessment to inform understanding of biological function and the design of therapeutic interventions.

Methodology:

Analyzes local sequence-to-structure fitness through torsion angle propensities with angles normalized against global minima and maxima, incorporates an energy normalization procedure, and uses conformational criteria derived from the Ramachandran plot; effectiveness was evaluated against experimental quality parameters across the full PDB and a subset of obsolete PDB structures.