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: 2018/03/21

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

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