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1. What is PONDEROSA-C/S?

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.

INPUTS: Here is what you will need to prepare before running PONDEROSA-C/S:
  1. Resonance assignment file. NMR-STAR file format (.str), XEASY proton file format (.prot), PIPP file format (.pipp) or SPARKY assignment table format (.shifts).

  2. Protein amino acid sequence file. In any one of three common formats: 3-letter-code with indices (.seq), FASTA 1-letter-code (.fasta), 3-letter or 1-letter in individual lines (.txt). Examples of each are given below.

  3. 3D-NOESY (13C-edited and/or 15N-edited): Both raw spectra and refined peak lists supported. Raw spectra should be in eother SPARKY (.ucsf) or NMRPipe (.pipe) format. Unrefined peak lists should be either SPARKY (.list) and XEASY (.peaks) format.

  4. {Optional} Distance restraints (.upl, .lol), torsion angle restraints (.aco), residual dipolar couplings (.rdc) and/or small angle X-ray scattering raw data (.dat)


OUTPUTS: Here is what you will get after a PONDEROSA-C/S run.

  1. A family of conformers in PDB format that represent the protein 3D structure calculated by CYANA.

  2. 2D structure analysis, solvent accessible surface (SAS), torsion angles (PHI, PSI) from STRIDE and TALOS relatives (TALOS, TALOS+, TALOS-N).

  3. MolProbity analysis file.

  4. Lists of assigned and unassigned peak lists from the 3D-NOESY spectra in SPARKY and XEASY format.

  5. Soon to be supported:

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2. What makes it so innovative?

NMR structures provide scientifically meaningful results, but NMR spectroscopy has been regarded as a harder and more expensive way of solving structures than X-ray crystallography. Thus, it is important to develop ways of making NMR more efficient and less expensive.

So, what makes PONDEROSA-C/S so innovative and distinctive?

  1. It is automated.

  2. Client-side and server-side are separated.

  3. Refinement tool for polishing your structure is provided.

  4. Supported by NMRFAM (National Magnetic Resonance Facility At Madison).

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3. Side-by-side comparison of the orignal PONDEROSA and PONDEROSA-C/S



PONDEROSA
PONDEROSA-C/S
OS
Linux
Any OS (user), Linux (server)
Installation
Hard (prerequisites)
Easy
Supported formats
Limited
Almost all existing formats
Nomenclature
HX
HX, MX, QX
NOESY
13C-edited aliphatic NOESY, 15N-edited NOESY
13C-edited aliphatic NOESY, 13C-edited aromatic NOESY, 15N-edited NOESY
Multiple NOESY
Sum intensities (limited)
Combinatorial (unlimited)
Different NOESY
13C first, 15N later. One-by-one.
More informative NOESY goes first, and balanced well
Folded NOESY
Not supported Supported
RDC, SAXS
Not supported
Supported
Scoring system
Procheck based
MolProbity based
Validation
PonderosaUI as a viewer
Fully supported with Ponderosa Analyzer
Refinement
Limited and manual
Fully supported with Ponderosa Analyzer
Performance
Good
Better

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Reference:

  1. Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. (2016) The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. Journal of Biomolecular NMR 65(2):51-57
  2. Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Wildman-Henzler K, Markley JL. (2016) Integrative NMR for biomolecular research. Journal of Biomolecular NMR 64(4):307-332
  3. Lee W, Stark JL, Markley JL. (2014) PONDEROSA-C/S: Client-server based software package for automated protein 3D structure determination. Journal of Biomolecular NMR  60(2-3):73-5
  4. Lee W, Kim JH, Westler WM, Markley JL (2011) PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics 27: 1727–1728

Last Updated: May 9, 2016
By Woonghee Lee (whlee@nmrfam.wisc.edu)


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