This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY cross-peaks and the three-dimensional structure of the protein in solution can be calculated automatically with CYANA.
[Question from NMRWiki Q&A forum] Using CYANA and ARIA to caluclate structure of protein
Using CYANA and ARIA to caluclate structure of protein
Could you please describe about advantages and disadvantages of CYANA2.1 and ARIA1.2 software to calculate the structure of protein ? which one can give best results ?
Check if somebody has answered this question on NMRWiki QA forum
nmrlearner
News from other NMR forums
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10-21-2011 10:04 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
nmrlearner
Journal club
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11-24-2010 08:49 PM
[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding?
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down.
In the end there is a message
****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look?
edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
nmrlearner
News from other NMR forums
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11-02-2010 11:22 PM
Structure Calculation Using CS-DP ROSETTA from NESG Wiki
Structure Calculation Using CS-DP ROSETTA
This is a copy of instructions for CS-DP Rosetta from NESG Wiki that was created on 8/20/19. Please go to the original post at http://www.nmr2.buffalo.edu/nesg.wiki/Structure_Calculation_Using_CS-DP_ROSETTA
for a more up-to-date version.
Introduction
The CS-DP-Rosetta approach merges the ideas of model generation using CS-Rosetta with model filtering by agreement to NOESY data via the DP-score from the RPF program to generate high accuracy protein structures. This hybrid approach uses both local backbone chemical shift data...
markber
BioNMR Wiki
0
08-20-2010 12:22 PM
structure refinement after cyana
Can anybody tell me, how to energy minimize a CYANA calculated average structure. I used model_minimize.inp from CNS, but is there any other method generally used by the CYANA users.
Also, how can I get the bonds, impropers and angle violation (rmsds) information on the CYANA calculated structures. Does CYANA has any program to do it.
Please help me with it.
Thank you.
sarun
NMR Questions and Answers
0
11-20-2008 03:41 AM
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
premprakash
NMR Questions and Answers
0
03-29-2007 02:33 PM
PASD: auto NOE assignment & structure calculation
Completely Automated, Highly Error-Tolerant Macromolecular Structure Determination from Multidimensional Nuclear Overhauser Enhancement Spectra and Chemical Shift Assignments
Kuszewski, J.; Schwieters, C. D.; Garrett, D. S.; Byrd, R. A.; Tjandra, N.; Clore, G. M.;
J. Am. Chem. Soc. 2004; 126(20); 6258-6273
http://pubs.acs.org/isubscribe/journals/jacsat/126/i20/figures/ja049786hn00001.gif
Abstract:
The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser...
Automated NMR structure calculation with CYANA.
Linear Mode
