ponderosa-c/s_logo


 Image Map Welcome to NMRFAM Ponderosa Web Server.

Please upload your packed_inputs.txt file from Ponderosa Client working directory.
In other way, you can use two-letter-code "c3" in NMRFAM-SPARKY for quick submission.
Your result will be back in a few minutes to hours depending on your settings.

Currently, NMRFAM Ponderosa Web Server accepts:
1) Any academic projects with 5 different options,
2) Collaborative projects with 8 different options.

[Click here to download Ponderosa Client program for input preparation]

* Current performance settings in NMRFAM Ponderosa Server BUILD: 2017/01/30

Any academic users
Collaborators
CPU
20
40
Tiers
1
2
Steps
4
5
Supported
Calculation
Engines
1. AUDANA automation
2. PONDEROSA-X refinement
3. Constraints only-X
4. Constraints only-X for final step
(Implicit Water Refinement)
5. Constraints only-X for final step
(Explicit Water Refinement)
* Additional options:
6. CYANA calculation
7. PONDEROSA refinement
8. Constraints only


1. Keep file name as packed_inputs.txt !!!
2. Set User Name and Key Phrase as guest if you are not NMRFAM collaborator.
[Constraints Only-X(2)], [PONDEROSA-X refinement]

User Name (or guest): 
Key Phrase (or guest):
packed_inputs.txt:

Use PACSY DB for better NOE assignment (recommended)
PDB ID: , CHAIN ID: 
Do not use any information from same sequence proteins

Type select PDB_ID,CHAIN_ID from PDBSEQ_DB in PACSY web server to check template coverage.
Check PACSY-ALIGN to user defined coordinate file to enhance automated NOE assignments.




* Check your running jobs here.
Your E-mail:


Please review chemical shift assignment quality results from ARECA.
You will receive
ARECA results right after submitting a job.



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. in press
  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: July 5, 2016
By Woonghee Lee (whlee@nmrfam.wisc.edu)

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