PONDEROSA-CS

PONDEROSA-CS performs semi-automated determination of protein three-dimensional structures from nuclear magnetic resonance (NMR) spectroscopy data.

Key Features:

• Component structure: Consists of three programs: Ponderosa Server for processing NMR data, Ponderosa Client as the client-side component, and Ponderosa Analyzer for visualization, validation, and refinement of structural models.
• Input requirements: Requires the protein sequence, a list of assigned chemical shifts, and Nuclear Overhauser effect (NOE) datasets, including 13C- and/or 15N-NOESY.
• NOE processing: Processes NOE data using a peak-picking approach with restricted shift assignments to derive distance constraints.
• Output: Produces assigned NOEs and three-dimensional (3D) structural models of the protein.

Scientific Applications:

• Protein structure determination: Applied to determine 3D structures of proteins from NMR data and demonstrated on proteins used in benchmarking such as the Critical Assessment of automated Structure Determination by NMR (CASP).

Methodology:

Processes NOE spectra with a peak-picking approach enhanced by restricting chemical shift assignments to generate NOE assignments and distance constraints.