Updated on 2021/05/21

写真a

 
OTA Motonori
 
Organization
Graduate School of Informatics Department of Complex Systems Science 2 Professor
Graduate School
Graduate School of Information Science
Graduate School of Informatics
Undergraduate School
School of Informatics Department of Natural Science Informatics
School of Informatics and Sciences
Title
Professor
Contact information
メールアドレス

Degree 1

  1. 博士(理学) ( 1996.10   早稲田大学 ) 

Research Areas 2

  1. Life Science / Biophysics  / Theoretical biology, Bioinformatics

  2. Informatics / Life, health and medical informatics  / Bioinformatics

Research History 5

  1. 東京工業大学 学術国際情報センター 助教授

    2002.4 - 2008.3

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    Country:Japan

  2. 国立遺伝学研究所 DDBJ・生命情報研究センター 助手

    1996.8 - 2002.3

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    Country:Japan

  3. 日本学術振興会 特別研究員(DC2)

    1996.4 - 1996.7

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    Country:Japan

  4. 蛋白工学研究所 研究員

    1994.4 - 1995.3

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    Country:Japan

  5. 東燃(株)総合研究所 研究員

    1990.4 - 1994.3

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    Country:Japan

Education 1

  1. Waseda University

    1994.4 - 1996.10

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    Country: Japan

 

Papers 52

  1. Crystal structure of human V-1 in the apo form Reviewed

    S. Takeda, R. Koike, T. Nagae, I. Fujiwara, A. Narita, Y. Maéda, M. Ota

    Acta. Cryst. F   Vol. 77   page: 13 - 21   2021.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S2053230X20016829

  2. Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail Reviewed

    S. Takeda, R. Koike, I. Fujiwara, A. Narita, M. Miyata, M. Ota, Y. Maéda

    J. Mol. Biol.     2021

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    Language:English   Publishing type:Research paper (scientific journal)  

  3. Knowledge-based strutural models of SARS-CoV-2 proteins and their complexes with potential drugs Reviewed

    A. Hijikata, C. Shionyu-Mitsuyama, S. Nakae, M. Shionyu, M. Ota, S. Kanaya, T. Shirai

    FEBS Lett.   Vol. 594   page: 1960 - 1973   2020.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/1873-3468.13806

  4. All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins Reviewed

    R. Koike, M. Ota

    Biophys. Physicobiol.   ( 16 ) page: 280-286   2019.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.2142/biophysico.16.0_280

  5. Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins Reviewed

    R. Koike, M. Amano, K. Kaibuchi, M. Ota

    Protein Sci.   Vol. 29   page: 564-571   2019.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3789

  6. MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers Reviewed

    S. Minami, K. Sawada, M. Ota, G. Chikenji

    Bioinformatics   Vol. 34   page: 3324-3331   2018.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/bioinformatics/bty369

  7. Using 1HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method Reviewed

    H. Okazaki, N. Matsuo, T. Tenno, N. Goda, Y. Shigemitsu, M. Ota, H. Hiroaki

    Protein Sci.   Vol. 27   page: 1821-1830   2018.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3485

  8. Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins Reviewed

    N. Matsuo, N. Goda, K. Shimizu, S. Fukuchi, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 19   page: 401   2018.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/ijms19020401

  9. Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding Reviewed

    E. Uemura, T. Niwa, S. Minami, K. Takemoto, S. Fukuchi, K. Machida, H. Imataka, T. Ueda, M. Ota, H. Taguchi

    Sci. Rep.   Vol. 8   page: 678   2018.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41598-017-18977-5

  10. Structural changes of homodimers in the PDB Reviewed

    R. Koike, T. Amemiya, T. Horii, M. Ota

    J. Str. Biol.     page: in press   2018

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jsb.2017.12.004

  11. Rules for connectivity of secondary structure elements of proteins: Two-layer αβ sandwiches Reviewed

    S. Minami, G. Chikenji, M. Ota

    Prot. Sci.   Vol. 26   page: 2257-2267   2017.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3285

  12. Itinerary profiling to analyze a large number of protein-folding trajectories Reviewed

    M. Ota, M. Ikeguchi, A. Kidera

    Biophys. Physicobiol.   Vol. 13   page: 295-304   2016.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi.org/10.2142/biophysico.13.0_295

  13. Interface property responsible for effective interactions of protean segments: Intrinsically disordered regions that undergo disorder-to-order transitions upon binding Reviewed

    D. Shaji, T. Amemiya, R. Koike R, M. Ota

    BBRC   Vol. 478   page: 123-127   2016.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1016/j.bbrc.2016.07.082

  14. Profile comparison revealed deviation from structural constraint at the positively selected sites Reviewed

    H. Oda , M. Ota, H. Toh

    Biosystems   Vol. 147   page: 67-77   2016.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1016/j.biosystems.2016.07.007

  15. Multiple-localization and hub proteins Reviewed

    M. Ota, H. Gonja, R. Koike, S. Fukuchi

    PLoS ONE   Vol. 11   page: e0156455   2016.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1371/journal.pone.0156455

  16. Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes Reviewed

    R. Koike, S. Takeda, Y. Maéda, M. Ota

    Proteins   Vol. 84   page: 948-956   2016.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1002/prot.25043

  17. Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in autism Reviewed

    M. Maekawa, Y. Iwayama, T. Ohnishi, M. Toyoshima, C. Shimamoto, Y. Hisano, T. Toyota, S. Balan, H. Matsuzaki, Y. Iwata, S. Takagai, K. Yamada, M. Ota, S. Fukuchi, Y. Okada, W. Akamatsu, M. Tsujii, N. Kojima, Y. Owada, H. Okano, N. Mori, T. Yoshikawa

    Sci. Rep.   Vol. 5   page: 16239   2015.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi:10.1038/srep16239

  18. Domain-motion enhanced (DoME) model for efficient conformational sampling of multi-domain proteins Reviewed

    C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita

    J. Phys. Chem. B   Vol. 119   page: 14584-14593   2015.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1021/acs.jpcb.5b07668

  19. A method for systematic assessment of intrinsically disordered protein regions by NMR Reviewed

    N. Goda, K. Shimizu, Y. Kuwahara, T. Noguchi, T. Ikegami, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 16   page: 15743-15760   2015.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/ijms160715743

  20. Hierarchical domain-motion analysis of conformational changes in Sarcoplasmic Reticulum Ca2+-ATPase Reviewed

    C. Kobayashi, R. Koike, M. Ota, Y. Sugita

    Proteins   Vol. 83   page: 746-756   2015.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/prot.24763

  21. An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study Reviewed

    N. Goda, N. Matsuo, T. Tenno, S. Ishino, Y. Ishino, S. Fukuchi, M. Ota, H. Hiroaki

    IDP   Vol. 3   page: 1-6   2015.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/21690707.2015.1011004

  22. Hierarchical description and extensive classification of protein structural changes by Motion Tree Reviewed

    R. Koike, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 426   page: 752-762   2014.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jmb.2013.10.034

  23. IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners Reviewed

    S. Fukuchi, T. Amemiya, S. Sakamoto, Y. Nobe, K. Hosoda, Y. Kado, SD. Murakami, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.   Vol. 42   page: D320-D325   2014.1

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  24. Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHMT2 and WIZ, in Japanese autism subjects Reviewed

    S. Balan, Y. Iwayama, M. Maekawa, T. Toyota, T. Ohnishi, M. Toyoshima, C. Shimamoto, K. Esaki, K. Yamada, Y. Iwata, K. Suzuki, M. Ide, M. Ota, S. Fukuchi, M. Tsujii, N. Mori, Y. Shinkai, T. Yoshikawa

    Molecular Autism     page: in the press   2014

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  25. Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening Reviewed

    T. Tenno, N. Goda, Y. Umetsu, M. Ota, K. Kinoshita, H. Hiroaki

    Molecules   Vol. 18   page: 9567-9581   2013.8

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  26. Substrate-shielding and hydrolytic reaction in hydrolases Reviewed

    Y. Kanematsu, R. Koike, T. Amemiya, M. Ota

      Vol. 81   page: 926-932   2013.2

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    Language:English   Publishing type:Research paper (scientific journal)  

  27. An assignment of intrinsically disordered regions of proteins based on NMR structures Reviewed

    M. Ota, R. Koike, T. Amemiya, T. Tenno, P. R. Romero, H. Hiroaki, A. K. Dunker, S. Fukuchi

    J. Str. Biol.   Vol. 181   page: 29-36   2013.1

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  28. Influence of structural symmetry on protein dynamics Reviewed

    Y. Matsunaga, R. Koike, M. Ota, J. Tame, A. Kidera

    PLos One   Vol. 7   page: e50011   2012.11

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  29. A nobel biclustering approach with iterative optimization to analyze gene expression data Reviewed

    S. Sutheworapong, M. Ota, H. Ohta, K. Kinoshita

    Adv. Appl. Bioinform. Chem.   Vol. 5   page: 23-59   2012.9

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  30. SCPC: A method to structurally compare protein complexes

    R. Koike, M. Ota

    Bioinformatics     page: in press   2012.2

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  31. PSCDB: a database for protein structural change upon ligand binding

    T. Amemiya, R. Koike, A. Kidera, M. Ota

    Nucleic Acids Res.     page: in press   2012

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  32. IDEAL: intrinsically disordered proteins with extensive annotations and literature

    S. Fukuchi, S. Sakamoto, Y. Nobe, SD. Murakami, T. Amemiya, K. Hosoda, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.     page: in press   2012

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    Language:English   Publishing type:Research paper (scientific journal)  

  33. SAHG, a comprehensive database of predicted structures of all human proteins Reviewed

    C. Motono, J. Nakata, R. Koike, K. Shimizu, M. Shirota, T. Amemiya, K. Tomii, N. Nagano, N. Sakaya, K. Misoo, M, Sato, A. Kidera, H. Hiroaki, T. Shirai, K. Kinoshita, T. Noguchi, M. Ota

    Nucleic Acids Res.   Vol. 39   page: D487   2011

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  34. Cover and spacer insertions: small non-hydrophobic accessories that assist protein oligomerization

    H. Nishi, R. Koike, M. Ota

    Proteins   Vol. 79   page: 2372-2379   2011

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  35. Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function Reviewed

    S. Takeda, R. Koike, Y. Nitanai, S. Minakata, Y. Maéda, M. Ota

    Phys. Biol.   Vol. 8   page: 035005   2011

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  36. Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design Reviewed

    Y. Matsuura, M. Ota, T. Tanaka, M. Takehira, K. Ogasahara, B. Bagautdinov, N. Kunishima, K. Yutani

    J. Biochem.   Vol. 148   page: 449-458   2010

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  37. Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state Reviewed

    H. Nishi, M. Ota

    Proteins   Vol. 78   page: 1563-1574   2010

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  38. Two distinct mechanisms for actin capping proteinregulationTwo distinct mechanisms for actin capping proteinregulation- steric and allosteric inhibitionsteric and allosteric inhibition Reviewed

    S. Takeda, S. Minakata, R. Koike, I. Kawahata, A. Narita, M. Kitazawa, M. Ota, T.Yamakuni, Y. Maéda, Y. Nitanai

    PLos Biol.   Vol. 8   page: e1000416   2010

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  39. Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold Reviewed

    R. Koike, A. Kidera, M. Ota

    Protein Sci.   Vol. 18   page: 2060-2066   2009

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  40. An evaluation of minimal cellular functions to sustain a bacterial cell Reviewed

    Y. Azuma, M. Ota

    BMC Syst. Biol.   Vol. 3   page: 111   2009

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  41. An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    BMC Bioinformatics   Vol. 9   page: 344   2008

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  42. Protein structural change upon ligand binding correlates with enzymatic reaction mechanism Reviewed

    R. Koike, T. Amemiya, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 379   page: 397-401   2008

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  43. Unfolding pathways of goat α-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories Reviewed

    T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima and A. Kidera

    J. Mol. Biol.   Vol. 371   page: 1354-64   2007

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  44. Enhanced partial order curve comparison over multiple protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    Comput. Syst. Bioinformatics. Conf.   Vol. 6   page: 299-310   2007

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  45. A hyperthermophilic protein acquires function at the cost of stability Reviewed

    A. Mukaiyama, M. Haruki, M. Ota, Y. Koga, K. Takano and S. Kanaya

    Biochemistry   Vol. 24   page: 12673-12679   2006

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  46. Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis Reviewed

    M. Haruki, Y. Saito, M. Ota, K. Nishikawa, S. Kanaya

    J. Biotech.   Vol. 25   page: 512-522   2006

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  47. Design of λ Cro fold: solution structure of a monomeric variant of the de novo protein Reviewed

    Y. Isogai, Y. Ito, T. Ikeya, Y. Shiro, M. Ota

    J. Mol. Biol.   Vol. 354   page: 801-814   2005

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  48. P-cats: Prediction of catalytic residues in proteins from the tertiary structures Reviewed

    K. Kinoshita and M. Ota

    Bioinformatics   Vol. 21   page: 3570-3571   2005

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  49. Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry Reviewed

    Y. Asada, M. Sawano, K. Ogasahara, J. Nakamura, M. Ota, C. Kuroishi, M. Sugahara, K. Yutani, N. Kunishima

    J Biochem (Tokyo)   Vol. 138   page: 343-353   2005

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  50. Phylogeny of protein-folding trajectories reveals a unique pathway to native structure Reviewed

    M. Ota, M. Ikeguchi and A. Kidera

    Proc. Natl. Acad. Sci. USA   Vol. 101   page: 17658-17663   2004

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  51. Integrative annotation of 21,037 human genes validated by full-length cDNA clones Reviewed

    T. Imanishi et al.

    PLoS. Biol.   Vol. 2   page: E162   2004

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  52. The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus Reviewed

    Y. Hioki, K. Ogasahara K, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S. Kuramitsu, K. Yutani

    Eur. J. Biochem.   Vol. 271   page: 2624-2635   2004

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Books 1

  1. ドロプレット形成のデータベースと予測(相分離生物学の全貌 白木賢太郎編)

    太田元規,福地佐斗志( Role: Contributor)

    東京化学同人  2020.11 

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    Total pages:402   Responsible for pages:363-367   Language:Japanese Book type:Scholarly book

Industrial property rights 1

  1. タンパク質凍結保存用保護剤

    法人名大,産業技術総合研究所

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    Date applied:2015.1

    Announcement no:WO 2015/125501  Date announced:2015.8

    Country of applicant:Foreign country   Country of acquisition:Foreign country

 

Teaching Experience (On-campus) 13

  1. First Year Seminar A

    2020

  2. Introduction to Biophysics Ib

    2020

  3. バイオインフォマティクス特論2

    2020

  4. バイオインフォマティクス特論1

    2020

  5. 複雑系科学特論1

    2020

  6. Complex Systems Exercise 4

    2020

  7. Physical and Life Science Informatics 10

    2020

  8. Physical and Life Science Informatics 3

    2020

  9. Simulation Science 2

    2020

  10. Informatics 4

    2020

  11. Nature as Information System 1:Life

    2020

  12. 計算科学フロンティア

    2020

  13. 大規模複雑系計算特論2

    2020

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