Using a model structure to accelerate NOESY data interpretation and structure calculation

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Woonghee Lee

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May 14, 2020, 3:49:07 PM5/14/20

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Dear Anon,

You can use your PDB file from CS-Rosetta as a restraint in the restraint section in Ponderosa Client. That will back-simulate distance restraints from CS-Rosetta and use that knowledge to assign NOESY data.

Best,

Woonghee

Therefore, I have a question regarding NOE assignments that I was hoping that you could answer if you have time, or if you could point me in the right direction. I have obtained a tentative structure for my protein by uploading my backbone assignments to the CS-Rosetta server, which I am sure you are very familiar with, and now I want to use this tentative structure and sort of validate it with NOESY data. I have acquired an N-resolved 3D-NOESY-HSQC and a 2D H-H NOESY for this purpose. Is there a smooth way to use the output of CS-Rosetta and sort of integrate it with the raw NOESY spectra to do an automated NOE assignment? I know that I can for instance use the PONDEROSA client to upload backbone chemical shift assignments and the raw NOESY spectra for automated NOE assignment but I specifically would like to use the output of CS-Rosetta, and am wondering if this is even possible? I would greatly appreciate any suggestion.

Thanks in advance. Best regards,

================================================

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Scientist ( - July 2020)

and

Principal Investigator

National Magnetic Resonance Facility at Madison (NMRFAM)

and Biochemistry Department

University of Wisconsin-Madison

DeLuca Biochemistry Laboratories

433 Babcock Drive Rm B160E

Madison, WI USA 53706-1544

wh...@nmrfam.wisc.edu, wle...@wisc.edu