ProSA-web

ProSA-web assesses 3D protein structures to validate and guide refinement of experimentally determined and computationally predicted models, supporting X-ray crystallography and nuclear magnetic resonance (NMR) studies.

Key Features:

• Validation of experimental and predicted structures: Provides independent computational assessment of experimentally determined and theoretical protein models.
• Knowledge-based mean fields: Uses knowledge-based mean fields to evaluate the integrity of protein folds.
• Error detection: Identifies misfolded structures and erroneous segments within structural models.
• C-alpha trace compatibility: Operates on full atomic models and on reduced representations including C-alpha traces.
• Quality scores and energy plots: Computes quality scores and energy plots that are contextualized against all known protein structures.
• Support for modeling: Facilitates structure prediction and modeling by providing fold-quality assessments that complement experimental data.

Scientific Applications:

• X-ray crystallography validation: Validation of protein structures determined by X-ray crystallography.
• NMR structure validation: Validation of protein structures derived from nuclear magnetic resonance (NMR) spectroscopy.
• Theoretical model assessment: Assessment of protein models generated by theoretical calculations and structure prediction.
• Model refinement guidance: Identification of problematic regions to guide refinement of protein structural models.

Methodology:

Employs knowledge-based mean fields to evaluate protein fold integrity, computes quality scores and energy plots contextualized against all known protein structures, and can analyze models using only C-alpha traces.