TY - JOUR
T1 - KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
AU - Kobayashi, Naohiro
AU - Iwahara, Junji
AU - Koshiba, Seizo
AU - Tomizawa, Tadashi
AU - Tochio, Naoya
AU - Güntert, Peter
AU - Kigawa, Takanori
AU - Yokoyama, Shigeyuki
N1 - Funding Information:
Acknowledgements We thank Drs. Toshio Yamazaki, Yutaka Muto, Fumiaki Hayashi, Takashi Nagata, Fahu He, Yufeng Wei and Prof. Milton, H. Werner for their valuable comments and discussions, and Prof. Yo Matsuo for his helpful advice regarding the algorithm for the calculation of the solvent accessible surface area. We also thank Mr. Masatomo Tanaka and Dr. Takuma Kasai for providing the information from the structural analyses of human ubiquitin. This work was supported by the RIKEN Structural Genomics/Proteomics Initiative (RSGI), the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science and Technology of Japan.
PY - 2007/9
Y1 - 2007/9
N2 - 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.
AB - 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.
KW - CYANA
KW - High-throughput
KW - KUJIRA
KW - NMR
KW - NMRView
KW - Software
KW - Structure determination
UR - http://www.scopus.com/inward/record.url?scp=34547923673&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34547923673&partnerID=8YFLogxK
U2 - 10.1007/s10858-007-9175-5
DO - 10.1007/s10858-007-9175-5
M3 - Article
C2 - 17636449
AN - SCOPUS:34547923673
VL - 39
SP - 31
EP - 52
JO - Journal of Biomolecular NMR
JF - Journal of Biomolecular NMR
SN - 0925-2738
IS - 1
ER -