ArticleJournal of biomolecular NMR2007
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.
Article in Journal of biomolecular NMR, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 162 citations in OpenAlex.
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- Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3.Communications biology · 2024Article
- Design of complicated all-α protein structures.Nature structural & molecular biology · 2024Article
- Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity.The Journal of biological chemistry · 2023Article
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- Structural polymorphism of the PH domain in TFIIH.Bioscience reports · 2023Article
- Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.Nucleic acids research · 2022Article
- Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA.Nature communications · 2022Article
- Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.Protein science : a publication of the Protein Society · 2022Article
- ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems.Membranes · 2022Article
- Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome.iScience · 2022Article
- Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 fromACS omega · 2022Article
- Identification of a Proline-Kinked Amphipathic α-Helix Downstream from the Methyltransferase Domain of a Potexvirus Replicase and Its Role in Virus Replication and Perinuclear Complex Formation.Journal of virology · 2021Article
- Sensitivity-Enhanced Solid-State NMR Detection of Structural Differences and Unique Polymorphs in Pico- to Nanomolar Amounts of Brain-Derived and Synthetic 42-Residue Amyloid-β Fibrils.Journal of the American Chemical Society · 2021Article
- Glycyrrhizin Derivatives Suppress Cancer Chemoresistance by Inhibiting Progesterone Receptor Membrane Component 1.Cancers · 2021Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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