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NMR processing:
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NMR assignment:
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MARS
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Side-chains:
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NOEs:
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UNIO Candid
ASDP
Structure from NMR restraints:
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GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
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UNIO Shiftinspector
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CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
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RPF scores
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Chemical shifts:
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Vasco
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RDCs:
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Pseudocontact shifts:
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PSVS
MolProbity
SAVES2 or SAVES4
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MetaMQAPII
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STAN
Ramachandran Plot
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ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
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V-NMR
Flexibility from structure:
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Methyl S2
B-factor
Molecular dynamics:
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Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
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Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
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Old 08-05-2008, 01:16 PM
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Default KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
Naohiro Kobayashi, Junji Iwahara, Seizo Koshiba, Tadashi Tomizawa, Naoya Tochio, Peter Güntert, Takanori Kigawa and Shigeyuki Yokoyama
Journal of Biomolecular NMR; 2007; 39(1) pp 31 - 52

Abstract:

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure.
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