NQ-Flipper

NQ-Flipper corrects erroneous side-chain amide rotamers of asparagine (Asn) and glutamine (Gln) in protein structures to improve structural accuracy for modeling and analysis.

Key Features:

• Knowledge-based potentials of mean force: Uses potentials of mean force derived from high-resolution protein crystal structures to evaluate rotamer energetics.
• Pairwise atom-atom interaction energy summation: Computes total interaction energy for Asn/Gln side-chain amide groups by summing pairwise atom-atom interaction energies within the local environment.
• Rotamer energy comparison: Identifies correct amide configurations by comparing computed energies between original and alternative rotamers.
• Self-consistent potential derivation: Derives self-consistent potential functions from high-resolution PDB crystal structure data.
• Refinement-correction cycle: Employs a refinement-correction cycle that converges to a set of potentials for reliable rotamer identification.
• Hydrogen-bond interaction consideration: Bases rotamer refinement on hydrogen bond interactions affecting Asn/Gln amide orientation.
• PDB input support: Accepts protein structures provided as PDB files or PDB codes for analysis.
• Per-residue energetics output: Reports interaction energies for all Asn/Gln residues and provides corrected rotamer assignments.

Scientific Applications:

• Protein structure refinement: Improves rotamer assignments in deposited PDB structures to increase structural accuracy during refinement.
• Protein structure prediction: Enhances side-chain amide orientation accuracy for computational structure prediction workflows.
• Molecular docking and modeling: Reduces rotamer-related errors that can affect docking, binding-site characterization, and molecular interaction studies.
• Structural database curation: Assists in identifying and correcting prevalent Asn/Gln rotamer errors within the Protein Data Bank.

Methodology:

Leverages knowledge-based potentials of mean force derived from high-resolution crystal structures; computes total interaction energies for Asn/Gln side-chain amides by summing pairwise atom-atom interaction energies within local environments; compares energies between original and alternative rotamers in a refinement-correction cycle that produces self-consistent potentials.