NMRe

NMRe refines NMR-derived protein structures using the Statistical Torsion Angle Potential (STAP) to improve structural accuracy guided by experimental NOE or inter-hydrogen distance restraints.

Key Features:

• Refinement protocol — NOE distance restraints: When provided, NMRe performs conventional NMR structure refinement using Nuclear Overhauser Effect (NOE) distance restraints.
• Refinement protocol — inter-hydrogen distance-based restraints: In the absence of explicit NOE data, NMRe generates NOE-like distance restraints from inter-hydrogen distances within the input structure.
• Energy function (STAP): NMRe leverages the knowledge-based Statistical Torsion Angle Potential (STAP) as the energy function for conformational optimization.
• Validation: The refinement was validated on a set of 20 NMR structures, with most quality assessment scores improving after refinement.
• Output formats: Refined models and validation results are produced as three-dimensional coordinates, secondary structure schemes, and numerical and graphical validation scores.

Scientific Applications:

• Protein structure accuracy: Improve the precision and reliability of NMR-derived protein models for downstream structural analysis.
• Functional and interaction studies: Support studies of protein function and molecular interactions by providing higher-quality structural models.
• Dynamics and flexible regions: Aid investigation of protein dynamics and flexible regions where NMR provides unique information and X-ray crystallography may be infeasible.

Methodology:

NMRe applies the Statistical Torsion Angle Potential (STAP) to iteratively optimize conformational space using either experimental NOE distance restraints or NOE-like restraints derived from inter-hydrogen distances.