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, Shigeyuki Yokoyama

Research output: Contribution to journalArticle

107 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)31-52
Number of pages22
JournalJournal of Biomolecular NMR
Volume39
Issue number1
DOIs
StatePublished - Sep 2007

Fingerprint

Chemical shift
Throughput
Nuclear magnetic resonance
Proteins
Genomics
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
Software
Datasets

Keywords

  • CYANA
  • High-throughput
  • KUJIRA
  • NMR
  • NMRView
  • Software
  • Structure determination

ASJC Scopus subject areas

  • Spectroscopy
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

Cite this

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. / Kobayashi, Naohiro; Iwahara, Junji; Koshiba, Seizo; Tomizawa, Tadashi; Tochio, Naoya; Güntert, Peter; Kigawa, Takanori; Yokoyama, Shigeyuki.

In: Journal of Biomolecular NMR, Vol. 39, No. 1, 09.2007, p. 31-52.

Research output: Contribution to journalArticle

Kobayashi, Naohiro ; Iwahara, Junji ; Koshiba, Seizo ; Tomizawa, Tadashi ; Tochio, Naoya ; Güntert, Peter ; Kigawa, Takanori ; Yokoyama, Shigeyuki. / KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. In: Journal of Biomolecular NMR. 2007 ; Vol. 39, No. 1. pp. 31-52.
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