KUJIRA - The integrated modules of KUJIRA for the integrated NMR structure analysis
The contribution of KUJIRA for the NMR studies :
Using KUJIRA and CYANA, the NMR structure analysis is now highly efficient :
Brief description :
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KUJIRA is a program for analysis of NMR, consisting of integrated and
networked modules working with a variety of graphical interfaces for systematic
and interactive analysis of NMR data by manual or automated assignments
of main-chain and side-chain signals. NMRView (Johnson, B. A., 1994) is
used in KUJIRA for displaying contour plots and controlling spectrum windows.
A module used for assessments of calculated structures, including the
functions for secondary structure detection, accessible surface area analysis,
Ramachandran and X1/X2 analysis, allows user to recognize the problematic
region of the structures readily. Another module in KUJIRA linked with
outputs of NOE assignments by CYANA calculations seamlessly controls chemical
shift table, spectrum windows and NOE assignment table as users to find
artifact or noise peaks among NOE peak table as well as miss-assignments
in the chemical shift table easily. These functions allow users not only
to achieve high completeness and accuracy of chemical shift table but
also to enormously save time for the structure refinement works.
The contribution of KUJIRA for the NMR studies :
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The protein3000 project, the software KUJIRA and CYANA were mainly used
for the structure determination studies. As you can find in PDB website,
the number of PDB structures that made use of KUJIRA reached more than
1152.
Using KUJIRA and CYANA, the NMR structure analysis is now highly efficient :
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The NMR stricture analysis based on the "step-by-step" procedure
has been a standard, by which the analysis normally requires 2-4 month
even for an well-experienced NMR scientist. The use of KUJIRA and CYANA
has greatly accelerated the analysis works and increased the reliability
of the signal assignments and determined structures.
Citing KUJIRA :
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If you publish work that made use of KUJIRA you can cite it as: KUJIRA,
a package of integrated modules for systematic and interactive analysis
of NMR data directed to high-throughput NMR structure studies Kobayashi
N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Gu"ntert P, Kigawa
T, Yokoyama S. J Biomol NMR. 39(1):31-52. (2007).
System Requirements:
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・Linux OS(RedHat, TurboLinux, Vine, etc)
・SGI IRIX6.5+
※ NMRView 5.0+ C language version