Software package for automated protein 3D structure determination.
PONDEROSA-C/S is a new software package developed at NMRFAM (National Magnetic Resonance Facility at Madison) for automated protein 3D structure determination. PONDEROSA-C/S is a successor of the PONDEROSA program, which utilizes information from prior assignments to automatically pick NOE peaks from 3D-NOESY (13C-edited and 15N-edited) spectra and uses the results as input for a series of AUDANA (Automated Database-Assisted NOE Assignment) or CYANA structure calculations with the goal of achieving a publishable quality solution structure. Compare to the original PONDEROSA, PONDEROSA-C/S offers improvements and many new innovations.
NMRFAM offers various software packages for high-throughput NMR. PONDEROSA-C/S is designed to interface with and extends other software packages such as, NMRFAM-SPARKY, PINE-NMR, PINE-SPARKY, ADAPT-NMR, and ADAPT-NMR Enhancer. The output from these packages is accepted as input to PONDEROSA-C/S, and, together, they offer an efficient pipeline for data collection, assignment, and structure determiantion.
PONDEROSA-C/S is designed to be accessible to persons who are not experts in NMR spectroscopy, and it offers a fast and easy way to determine protein 3D structures.
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