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N. Kobayashi · SciRah

Researcher profile · Semantic Scholar

N. Kobayashi

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N. Kobayashi — researcher profile on SciRah

h-index: 30
Works: 159
Citations: 2,598

Most-cited papers

Validation of Structures in the Protein Data Bank
S. Gore, E. Sanz-García, P. Hendrickx, A. Gutmanas +30 more
2017Structure242 citations Open access
Semantic Scholar
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
N. Kobayashi, J. Iwahara, S. Koshiba, T. Tomizawa +4 more
2007Journal of Biomolecular NMR168 citations
Semantic Scholar
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
Jasmine Y. Young, J. Westbrook, Zu-Kang Feng, Raul Sala +45 more
2017Structure136 citations Open access
Semantic Scholar
Structural insight into the zinc finger CW domain as a histone modification reader.
F. He, T. Umehara, Kohei Saito, T. Harada +13 more
2010Structure125 citations Open access
Semantic Scholar
Structure, interaction and real‐time monitoring of the enzymatic reaction of wild‐type APOBEC3G
A. Furukawa, T. Nagata, A. Matsugami, Yuichiro Habu +6 more
2009EMBO Journal122 citations Open access
Semantic Scholar
Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions
Takako Ohyama, T. Nagata, K. Tsuda, N. Kobayashi +4 more
2011Nucleic Acids Research93 citations Open access
Semantic Scholar
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
A. Kinjo, G. Bekker, H. Wako, S. Endo +12 more
2017Protein Science92 citations Open access
Semantic Scholar
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
K. Tsuda, Kanako Kuwasako, Mari Takahashi, T. Someya +10 more
2009Nucleic Acids Research79 citations Open access
Semantic Scholar
Structural basis for the dual RNA-recognition modes of human Tra2-β RRM
K. Tsuda, T. Someya, Kanako Kuwasako, Mari Takahashi +14 more
2010Nucleic Acids Research74 citations Open access
Semantic Scholar
Structures of the first and second double‐stranded RNA‐binding domains of human TAR RNA‐binding protein
S. Yamashita, T. Nagata, M. Kawazoe, C. Takemoto +8 more
2011Protein Science72 citations Open access
Semantic Scholar
Structural insight into the interaction of ADP‐ribose with the PARP WWE domains
F. He, K. Tsuda, Mari Takahashi, Kanako Kuwasako +8 more
2012FEBS Letters64 citations Open access
Semantic Scholar
Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists
T. Sugiki, N. Kobayashi, T. Fujiwara
2017Computational and Structural Biotechnology Journal62 citations Open access
Semantic Scholar
A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription
Yu-Feng Wei, Shaohua Liu, J. Lausen, Christopher Woodrell +6 more
2007Nature Structural &Molecular Biology54 citations
Semantic Scholar
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Daniel Schober, D. Jacob, Michael Wilson, Joseph A. Cruz +28 more
2018Analytical Chemistry53 citations Open access
Semantic Scholar
Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR
N. Wu, N. Kobayashi, K. Tsuda, S. Unzai +3 more
2020Scientific Reports51 citations Open access
Semantic Scholar
NMR Exchange Format: a unified and open standard for representation of NMR restraint data
A. Gutmanas, P. Adams, B. Bardiaux, H. Berman +21 more
2015Nature Structural &Molecular Biology51 citations Open access
Semantic Scholar
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition
T. Nagata, Sakura Suzuki, Ryuta Endo, M. Shirouzu +9 more
2008Nucleic Acids Research48 citations Open access
Semantic Scholar
BioMagResBank (BMRB) as a Resource for Structural Biology
Pedro Romero, N. Kobayashi, Jonathan R. Wedell, Kumaran Baskaran +9 more
2020Methods in molecular biology46 citations
Semantic Scholar
The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion apparatus.
Shino Mizuno, Hirokazu Amida, N. Kobayashi, S. Aizawa +1 more
2011Journal of Molecular Biology35 citations
Semantic Scholar
Robust folding of a de novo designed ideal protein even with most of the core mutated to valine
R. Koga, Mami Yamamoto, T. Kosugi, N. Kobayashi +3 more
2020Proceedings of the National Academy of Sciences of the United States of America33 citations Open access
Semantic Scholar
RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Kanako Kuwasako, Mari Takahashi, S. Unzai, K. Tsuda +11 more
2014Nature Structural &Molecular Biology33 citations
Semantic Scholar
Exploration of novel αβ-protein folds through de novo design
S. Minami, N. Kobayashi, T. Sugiki, T. Nagashima +4 more
2021bioRxiv32 citations Open access
Semantic Scholar
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
Ayesha Wickramasinghe, Yiling Xiao, N. Kobayashi, Songlin Wang +4 more
2021Journal of the American Chemical Society31 citations Open access
Semantic Scholar
An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database
N. Kobayashi, Yoko Harano, N. Tochio, Eiichi Nakatani +7 more
2012Journal of Biomolecular NMR31 citations Open access
Semantic Scholar
Plastic roles of phenylalanine and tyrosine residues of TLS/FUS in complex formation with the G-quadruplexes of telomeric DNA and TERRA
Keiko Kondo, T. Mashima, T. Oyoshi, R. Yagi +4 more
2018Scientific Reports30 citations Open access
Semantic Scholar
The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif.
N. Xu, N. Tochio, Jing Wang, Yu Tamari +6 more
2014Biochemistry30 citations Open access
Semantic Scholar
Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA
Ryo Iwaoka, T. Nagata, K. Tsuda, T. Imai +3 more
2017Molecules29 citations Open access
Semantic Scholar
Solution structure of the cysteine‐rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily
F. He, W. Dang, Kohei Saito, S. Watanabe +6 more
2009Protein Science27 citations Open access
Semantic Scholar
Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.
F. He, Kohei Saito, N. Kobayashi, T. Harada +8 more
2009Journal of Molecular Biology27 citations
Semantic Scholar
Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA.
Jing Wang, N. Tochio, Aya Takeuchi, Jun-ichi Uewaki +2 more
2013Biochemical and Biophysical Research Communications - BBRC26 citations Open access
Semantic Scholar
Noise peak filtering in multi‐dimensional NMR spectra using convolutional neural networks
N. Kobayashi, Y. Hattori, Takashi Nagata, Shoko Shinya +3 more
2018Bioinform.25 citations Open access
Semantic Scholar
Solution structure of the RNA binding domain in the human muscleblind‐like protein 2
F. He, W. Dang, C. Abe, K. Tsuda +16 more
2009Protein Science23 citations Open access
Semantic Scholar
Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display
T. Nagata, Kie Shirakawa, N. Kobayashi, Hirokazu Shiheido +6 more
2014PLoS ONE20 citations Open access
Semantic Scholar
Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.
Kanako Kuwasako, Mari Takahashi, N. Tochio, C. Abe +12 more
2008Biochemistry19 citations
Semantic Scholar
Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions
S. Ohnishi, Kimmo Pääkkönen, S. Koshiba, N. Tochio +9 more
2009Proteins: Structure, Function, and Bioinformatics18 citations
Semantic Scholar
Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner
N. Nakayama, G. Sakashita, T. Nagata, N. Kobayashi +8 more
2020Biomedicines15 citations Open access
Semantic Scholar
Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA.
Jing Wang, N. Tochio, Aya Takeuchi, Jun-ichi Uewaki +2 more
2013Biochemical and Biophysical Research Communications - BBRC15 citations
Semantic Scholar
How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?
Tatsuya Yamada, Tomohiko Hayashi, Simon Hikiri, N. Kobayashi +5 more
2019Journal of Chemical Information and Modeling14 citations Open access
Semantic Scholar
Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization
K. Matsumura, Takushi Shimomura, Y. Kubo, Takayuki Oka +11 more
2020bioRxiv13 citations Open access
Semantic Scholar
Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints
K. Furuita, Saori Kataoka, T. Sugiki, Y. Hattori +5 more
2014Journal of Biomolecular NMR13 citations
Semantic Scholar
Structure and real-time monitoring of the enzymatic reaction of APOBEC3G which is involved in anti-HIV activity.
A. Furukawa, T. Nagata, A. Matsugami, Yuichiro Habu +6 more
2009Nucleic Acids Symposium Series12 citations Open access
Semantic Scholar
Solution structures of the double‐stranded RNA‐binding domains from rna helicase A
T. Nagata, K. Tsuda, N. Kobayashi, M. Shirouzu +4 more
2012Proteins: Structure, Function, and Bioinformatics9 citations
Semantic Scholar
Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.
S. Bala, Shoko Shinya, Arpita Srivastava, M. Ishikawa +6 more
2020Biochimica et Biophysica Acta - General Subjects7 citations Open access
Semantic Scholar
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
M. Yokochi, N. Kobayashi, E. Ulrich, A. Kinjo +7 more
2016Journal of Biomedical Semantics7 citations Open access
Semantic Scholar
Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment
Kanako Kuwasako, N. Nameki, K. Tsuda, Mari Takahashi +14 more
2016Protein Science7 citations Open access
Semantic Scholar
A robust method for quantitative identification of ordered cores in an ensemble of biomolecular structures by non-linear multi-dimensional scaling using inter-atomic distance variance matrix
N. Kobayashi
2014Journal of Biomolecular NMR7 citations
Semantic Scholar
Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3
K. Tsuda, Kanako Kuwasako, T. Nagata, Mari Takahashi +6 more
2014Proteins: Structure, Function, and Bioinformatics6 citations
Semantic Scholar
Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA
Ryo Iwaoka, T. Nagata, K. Tsuda, T. Imai +3 more
2017Biomolecular NMR Assignments5 citations
Semantic Scholar
1H, 15N and 13C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein
Saori Kataoka, K. Furuita, Y. Hattori, N. Kobayashi +4 more
2014Biomolecular NMR Assignments5 citations
Semantic Scholar
Solution structure of the splicing factor motif of the human Prp18 protein
F. He, M. Inoue, T. Kigawa, Mari Takahashi +8 more
2012Proteins: Structure, Function, and Bioinformatics4 citations
Semantic Scholar

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