PRAS

PRAS repairs and analyzes protein structures in PDB and mmCIF formats to correct sequence microheterogeneity, rotamers, missing side chains, heavy atoms, and hydrogen atoms, assign secondary structure from backbone amide-amide interactions, and produce validation outputs including Ramachandran plots and corrected PDB files.

Key Features:

• Structure repair and atom addition: Identifies and corrects sequence microheterogeneity, rotamers, and missing side chains, heavy atoms, and hydrogen atoms in PDB and mmCIF structures.
• Automated error correction and logging: Generates a detailed log file documenting identified irregularities and the corrective actions applied to the input structure.
• Secondary structure assignment: Assigns secondary structure elements based on amide-amide interactions within the corrected backbone.
• Ramachandran plot generation: Produces Ramachandran plots for general, glycine, proline, and pre-proline residue classes to evaluate backbone conformations.
• Analytical outputs: Outputs an error-corrected PDB file and plots showing percentages of secondary structure elements and Ramachandran distributions.
• Format compatibility: Supports structures in PDB format and can address analogous structural issues in the mmCIF format.

Scientific Applications:

• Structural biology: Improves the quality of experimental PDB/mmCIF models for interpretation of protein folding and function.
• Model validation and quality assessment: Provides validation metrics and plots (Ramachandran distributions and secondary structure percentages) for assessing model geometry and completeness.
• Computational modeling and drug design: Produces corrected input structures suitable for downstream modeling, docking, and computational chemistry workflows.
• Protein engineering: Supplies repaired structures with corrected rotamers and missing atoms for design and mutational analyses.
• Bioinformatics analyses: Supplies validated structural data for incorporation into bioinformatics pipelines and structural databases.

Methodology:

The workflow comprises an initial set of subroutines that identify and correct structural issues, followed by assignment of secondary structures based on corrected backbone amide-amide interactions.