PONDEROSA

Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments


Synopsis

Software package for automated protein 3D structure determination.

Description

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-SPARKYPINE-NMRPINE-SPARKYADAPT-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.

URL

http://ponderosa.nmrfam.wisc.edu/introduction.html

Versions

NMRbox Version Software Version
1.0.0 Build_05-27-2016,
2.0.0 Build_11-03-2016,
3.0.0 Build_11-03-2016, Build_06-22-2017,

Keywords

  • Structure Determination

Citations

PONDEROSA-C/S: client--server based software package for automated protein 3D structure determination
Lee Woonghee, Stark Jaime L, Markley John L,
Journal of biomolecular NMR. 2014; 60(2-3): 73--75