2020年1月12日更新

Papers (peer reviewed)

  1. Yuki Kagaya, Ryuhei Minei, Ha T. T. Duong, Binh T. N. Le, Lua T. Dang, Trang T. H. Tran, Hoa T. Nguyen, Kengo Kinoshita, Kei Yura, Atsushi Ogura, Oanh T. P. Kim (2020) Metagenome sequences from the environment of diseased otter clams, Lutraria rhynchaena, from a farm in Vietnam. Microbiology Resource Announcements, 9, e01068-19.
  2. Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima. (2019) A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports, 9, 19585. doi:10.1038/s41598-019-55069-y
  3. Yamauchi, Y., Konno, M., Yamada, D., Yura, K., Inoue, K., Beja, O., Kandori, H. (2019) Engineered functional recovery of microbial rhodopsin without retinal-binding lysine. Photochemistry and Photobiology, 95, 1116-1121.
  4. Mouhib, H., Higuchi, A., Abeln, S., Yura, K., Feenstra, K.A. (2019) Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling. F1000Research, 8, 322.
  5. Sakamoto, M., Suzuki, H. Yura, K. (2019) Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins. Biophysics and Physicobiology, 16, 68-79.
  6. Ohtaka-Maruyama, C., Okamoto, M. Endo, K., Oshima, M., Kaneko, N., Yura, K., Okado, H., Miyata, T., Maeda, N. (2018) Synaptic transmission from subplate neurons controls radial migration of neocortical neurons. Science, 360(6386), 313-317.
  7. Higuchi, A., Nonaka, N., Yura, K. (2018) iMusta4SLC: Database for the structural property and variations of solute carrier transporters. Biophysics and Physicobiology, 15, 94-103.
  8. Tamura, R., Takeda, M., Sakaue, M., Yoshida, A., Ohi S., Hirano, K., Hayakawa, T., Hirohashi, N., Yura, K., Chiba, K. (2018) Starfish Apaf-1 activates effector caspase-3/9 upon apoptosis of aged eggs. Scientific Reports, 1611 (14 pages).
  9. Mizutani, H., Sugawara, H., Buckle, A.M., Sangawa, T., Miyazono, K., Ohtsuka, J., Nagata, K., Shijima, T., Nosaki, S., Xu, Y., Wang, D., Hu, X., Tanokura, M., Yura, K. (2017) REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC Structural Biology, 17, 4 (8 pages).
  10. Masakiyo, Y., Ogura, A., Ichihara, K., Yura, K., Shimada, S. (2016) Candidate key genes for low-salinity adaptation identified by RNA-seq comparison between closely related Ulvarian species in marine and brackish waters. Algal Resources, 9(2), 61-76.
  11. Gojobori, T. Ikeo, K., Katayama, Y., Kawabata, T., Kinjo, AR., Kinoshita, K., Kwon, Y., Migita, O., Mizutani, H., Muraoka, M., Nagata, K., Omori, S., Sugawara, H., Yamada, D, Yura, K. (2016) VaProS: A Database-Integration Approach for Protein/Genome Information Retrieval. Journal of Structural and Functional Genomics, 17(4), 69-81.
  12. Suzuki, Y., Yura, K. (2016) Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state. Biophysics and Physicobiology, 13, 127-134.
  13. Hayashi, K., Kawai, Y.L., Yura, K., Yoshida, M., Ogura, A., Hata, K., Nakabayashi, K., Okamura, K. (2016) Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans. Mitochondrial DNA, 27(3), 1842-1843.
  14. Aoto, S., Yura, K. (2015) Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins. Biophysics and Physicobiology, 12, 103-116.
  15. Inoue, K., Urushibara, K., Kanai, M., Yura, K., Fujii, S., Hashimoto, Y., Ishigami-Yuasa, M., Mori, S., Kawachi, E., Matsumura, M., Hirano, T., Kagechika, H., Tanatani, A. (2015) Design and synthesis of 4-benzyl-1-(2H)-phthalazinone derivatives as novel androgen receptor antagonists. European Journal of Medicinal Chemistry, 102, 310-319.
  16. Takahashi, K., Yoshida, K., Yura, K., Ashihara, H., Sakuta, M. (2015) Biochemical Analysis of Phytolacca DOPA Dioxygenase. Natural Product Communications, 10, 717-719.
  17. Hijikata, A., Yura, K., Ohara, O., Go, M. (2015) Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain. Meta Gene, 4, 92-106.
  18. Hori-Tanaka, Y., Yura, K., Takai-Igarashi, T., Tanaka, H. (2015) Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function. Steroids, 96, 81-88.
  19. Kamijyo, A., Yura, K., Ogura, A. (2015) Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure. Gene, 555 (2), 73-79.
  20. Kawai, Y.L., Yura, K., Shindo, M., Kusakabe, R., Hayashi, K., Hata, K., Nakabayashi, K., Okamura, K. (2015) Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum. Mitochondrial DNA, 25(6), 863-864.
  21. Kuppuraj, G., Kruise, D., Yura, K. (2014) Conformational behaviour of flavin adenine dinucleotide: Conserved stereochemistry in bound and free states. The Journal of Physical Chemistry B, 118 (47), 13486-13497.
  22. Kato, Y.S., Yagi, T., Harris, S.A., Ohki, S., Yura, K., Shimizu, Y., Honda, S., Kamiya, R., Burgess, S.A., Tanokura, M. (2014) Structure of the microtubule-binding domain of flagellar dynein. Structure, 22 (11) 1628-1638.
  23. Yoshida, M., Yura, K., Ogura, A. (2014) Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Scientific Reports, 4, 4256.
  24. Masui,R., Takahata, Y., Inoue, M., Iio, Y., Okanishi, H., Kim, K., Nakagawa, N., Yura, K., Kuramitsu, S. (2013) Structural insights of post-translational modification sites in the proteome of Thermus thermophilus. Journal of Structural and Functional Genomics, 15(3), 137-151
  25. Terui, H., Tachikawa, T., Kakuta, M., Nishimura, Y., Yatsuoka, T., Yamaguchi, K., Yura, K., Akagi, K. T (2013) Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients. Oncology Reports, 30(6), 2909-2916.
  26. Hoshina, S., Yura, K., Teranishi, H., Kiyasu, N., Tominaga, A., Kadoma, H., Nakatsuka, A., Kunichika, T., Obuse, C., Waga, S. (2013) Human Origin Recognition Complex Binds Preferentially to G-Quadruplex-Preferable RNA and Single-Stranded DNA. Journal of Biological Chemistry, 288(42), 30161-30171.
  27. Terui, H., Akagi, K., Kawame, H., Yura, K. (2013) CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. Journal of Biomedical Science, 20, 25.
  28. Takai, T., Higaki, K., Aguilar-Moncayo, M., Mena-Barragan, T., Hirano, Y., Yura, K., Yu, L., Ninomiya, Garcia-Moreno, H.M.I., Sakakibara, Y., Ohno, K., Nanba, E., Mellet, C.O., Fernandez, J.M.G., Suzuki, Y. (2013) A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis. Molecular Therapy, 21(3), 526-532.
  29. Kobayashi, E., Yura, K., Nagai, Y. (2013) Distinct Conformation of ATP Molecule in Solution and on Protein. BIOPHYSICS, 9, 1-12.
  30. Aguilar-Moncayo, M., Takai, T., Higaki, K., Mena-Barragan T., Hirano, Y., Yura, K., Li, L., Yu, Y., Ninomiya, H., Garcia-Moreno, M.I., Ishii, S., Sakakibara, Y., Ohno, K., Nanba, E., Oritz Mellet, C., Garcai Fernandez, J.M., Suzuki, Y. (2012) Tuning glycosidase inhibition through aglycone interactions: pharmacological chaperones for Fabry disease and GM1 gangliosidosis. Chem. Commun., 48, 6514-6516.
  31. Hijikata, A., Yura, K., Noguti, T., Go, M. (2011) Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins: Structure, Function, and Bioinformatics, 79(6), 1868-1877.
  32. Yura, K., Hayward, S. (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25(23), 3108-3113 (open access). (Google Scholar Cited by ... )
  33. Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M. (2009) RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant and Cell Physiology, 50 (11), 1865-1873 (open access).
  34. Yura, K., Go, M. (2008) Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biology, 8, 79 (open access). (Google Scholar Cited by ... )
  35. Yura, K., Miyata, Y., Arikawa, T., Higuchi, M., Sugita, M. (2008) Characteristics and prediction of RNA editing sites in transcripts of the moss Takakia lepidozioides chloroplast. DNA Research, 15 (5), 309-321 (open access). (Google Scholar Cited by ... )
  36. Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., Yura, K. (2008) Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal mode analysis. Biophysical Journal, 95 (6), 2895-2908. (Google Scholar Cited by ... )
  37. Miyazawa, Y., Nishioka, H., Yura, K., Yamato, T. (2008) Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. Biophysical Journal, 94 (6), 2194-2203.(Google Scholar Cited by ... )
  38. Genome Information Integration Project and H-Invitational 2 consortium (Yura, K. is the 66th / 138 authors). (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 36, D793-D799 (open access). (Google Scholar Cited by ...)
  39. Kono, H., Yuasa, T., Nishiue, S., Yura, K. (2008) coliSNP database server mapping nsSNPs on protein structures. Nucleic Acids Research, 36, D409-D413 (open access). (Google Scholar Cited by ...)
  40. Gong, X., Nakamura, K., Yu, H., Yura, K., Go, N. (2007) BAAQ: An infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Transactions on Information Technology in Biomedicine, 11 (4), 428-434.
  41. Yura, K., Yamaguchi, A., Go, M. (2006) Coverage of whole proteome by structural genomics observed through protein homology modeling database. Journal of Structural and Functional Genomics, 7 (2), 65-76 (open access). (Google Scholar Cited by ...)
  42. Kim, T.P.O., Yura, K., Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Research, 34 (22), 6450-6460 (open access). (Google Scholar Cited by ...) (access status in NAR)
  43. Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T., Go, M. (2006) Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene, 380 (2), 63-71. (Google Scholar Cited by ... )
  44. Takeda, J., Suzuki, Y., Nakao, M., Barrero, R., Koyanagi, K., Jin, L., Motono, C., Hata, H., Isogai,T., Nagai, K., Otsuki, T., Kuryshev, V., Shionyu, M., Yura, K., Go, M., Thierry-Mieg, J., Thierry-Mieg, D., Wiemann, S., Nomura, N., Sugano, S., Gojobori, T., Imanishi, T. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Research, 34 (14), 3917-3928 (open access). (Google Scholar Cited by ...)
  45. Metsugi, S., Uenoyama, A., Adan, J., Miyata, M., Yura, K., Kono, H., Go, N. (2005) Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile. BIOPHYSICS, 1, 33-43 (open access). (Google Scholar Cited by ...)
  46. Kim, T.P.O., Yura, K., Go, N., Harumoto, T. (2005) Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions. Gene, 346, 277-286, (Erratum). (Google Scholar Cited by ...)
  47. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, T., Tanino, M., Yura, K., et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2 (6), 0856-0875 (open access). (Google Scholar Cited by ...)
  48. Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., Kobayashi, H. (2004) Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex. Journal of Biological Chemistry, 279 (25), 26619-26626 (open access). (Google Scholar Cited by ...)
  49. Kim, T.P.O., Yura, K., Go, N., Harumoto, T. (2004) Highly divergent actins from Karyorelictean, Heterotrich and Litostome Ciliates. Journal of Eukaryotic Microbiology, 51 (2), 227-233. (Google Scholar Cited by ...)
  50. Yamaguchi, A.,Iida, K., Matsui, N., Tomoda, S., Yura, K., Go, M. (2004) Het-PDB Navi. : A database for protein-small molecule interactions. Journal of Biochemistry (Tokyo) 135 (1), 79-84. (Google Scholar Cited by ...)
  51. Nakamura, K., Kawabata, T., Yura, K., Go, N. (2003) Novel types of two-domain multi-copper oxidases: Possible missing links in the evolution FEBS Letters, 553 (3), 239-244. (Google Scholar Cited by ...)
  52. Yamaguchi, A., Iwadate, M., Suzuki, E., Yura, K., Kawakita, S., Umeyama, H., Go, M. (2003) Enlarged FAMSBASE: 3D protein structure models of genome sequences for 41 species. Nucleic Acids Research, 31 (1), 463-468 (open access). (Google Scholar Cited by ...)
  53. Ahsan M.M., Kaneko, S., Wang, Q., Yura, K., Go, M., Hayashi K. (2001) Capacity of Thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases. Enzyme Microb. Technol., 28 (1), 8-15. (Google Scholar Cited by ...)
  54. Yoshihara, S., Geng, X.X., Okamoto, S., Yura, K., Murata, T., Go M., Ohmori, M., Ikeuchi, M. (2001) Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiology, 42(1), 63-73. (Google Scholar Cited by ...)
  55. Kaneko, S., Iwamatsu, S., Kuno, A., Fujimoto, Z., Sato, Y., Yura, K., Go, M., Mizuno, H., Taira, K., Hasegawa, T., Kusakabe, I., Hayashi, K. (2000) Module shuffling of a family F/10 xylanase: replacement of modules M4 and M5 of the FXYN of Streptomyces olivaceoviridis E-86 with those of the Cex of Cellulomonas fimi. Protein Engineering, 13 (12), 873-879 (open access). (Google Scholar Cited by ...)
  56. Kikuchi, H., Wako, H., Yura, K., Go, M., Mimuro, M. (2000) Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis. Biophysical Journal, 79 (3), 1587-1600 (open access). (Google Scholar Cited by ...)
  57. Kaneko, S., Kuno, A., Fujimoto, Z., Shimizu, D., Machida, S., Sato, Y., Yura, K., Go, M., Mizuno, H., Taira, K. , Kusakabe, I. and Hayashi, K. (1999) An investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis. FEBS Letters, 460 (1), 61-66. (Google Scholar Cited by ...)
  58. Sato, Y., Niimura, Y., Yura, K., Go, M. (1999) Module-intron correlation and intron sliding in family F/10 xylanase genes. Gene, 238 (1), 93-101. (Google Scholar Cited by ...)
  59. Yura, K., Toh, H., Go, M. (1999) Putative mechanism of natural transformation as deduced from genome data. DNA Research, 6 (2), 75-82 (open access). (Google Scholar Cited by ...)
  60. Yura, K., Shionyu, M., Kawatani, K., Go, M. (1999) Repetitive use of a phosphate-binding module in DNA polymerase beta, Oct-1 POU domain and phage repressors. Cellular and Molecular Life Sciences, 55 (3), 472-486. (Google Scholar Cited by ...)
  61. Yura, K., Go, M. (1997) The homeodomain-like putative product of plastid genome: A possible role in plastid differentiation. Res. Comm. Biochem. Cell & Mol. Biol., 1 (1), 79-81. (Google Scholar Cited by ...) (publisher site)
  62. Nakashima, T. Sekiguchi, T., Sunamoto, H., Yura, K., Tomoda, S., Go, M., Kere, J., Schlessinger, D., Nishimoto, T. (1994) Structure of the human CCG1 gene: relationship between the exons/introns and functional domain/modules of the protein. Gene, 141 (2), 193-200. (Google Scholar Cited by ...)
  63. Koga, H., Sagara, Y., Yaoi, T., Tsujimura, M., Nakamura, K., Sekimizu, K., Makino, R., Shimada, H., Ishimura, Y., Yura, K., Go, M., Ikeguchi, M., Horiuchi, T. (1993) Essential role of the Arg112 residue of cytochrome P450cam for election transfer from reduced putidaredoxin. FEBS Letters, 331 (1-2), 109-113. (Google Scholar Cited by ...)
  64. Yura, K., Tomoda, S., Go, M. (1993) Repeat of a helix-turn-helix module in DNA binding proteins. Protein Engineering, 6 (6), 621-628. (Google Scholar Cited by ...)

International Conference Proceedings (peer reviewed)

  1. Yura, K. (2008) Prediction of Protein-RNA, Protein-Protein and Protein-Ligand Interfaces Based on Protein Sequences and 3D-Structures, in the Proceedings of International Symposium on Frontiers of Computational Science 2008 (eds. Yukio Kaneda, Masaki Sasai, Kanta Tachibana), pp.77-86.
  2. Go, M., Yura, K., Shionyu, M. (2007) Contribution of computational biology and structural genomics to understand genome and transcriptome. "Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005)", (eds. Y. Kaneda, H. Kawamura and M. Sasai), Springer, 75-80.
  3. Goto, J., Yasunaga, T., Nagai, R., Matsumoto, A., Yura, K., Takagi, J., Iwasaki, K. (2006) Toward the elucidation of the pathway of integrin conformational changes. Modern Scientific Instruments, Supplementary, 65-66.
  4. Iwasaki, K., Matsumoto, A., Yura, K., Goto, T., Yasunaga, T., Nagai, R., Takagi, J. (2006) The pathway of conformational changes of cell adhesion protein, integrin. Proceedings of the 16th International Microscopy Congress (IMC16), 234.
  5. Ishida, H., Matsumoto, A., Tsutsumi, Y., Yura, K. (2006) Conformational analysis of the structure of riosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations. Proceedings of the 16th International Microscopy Congress (IMC16), 242.
  6. Gong, X., Nakamura, K., Yura, K., Go, N. (2006) Toward Building Grid Applications in Bioinformatics. Proceedings of the Fourth Australasian Symposium on Grid Computing and e-Research (AusGrid 2006), 54, (eds. R. Buyya, and T. Ma) ACS, 17-23.
  7. Gong, X.J., Yura, K., Go, N. (2005) A grid-based system for integrating bioinformatics applications. Proceedings of the IADIS International Conference: Applied Computing 2005, 1, 551-558. (Google Scholar Cited by ...)

Books (non peer reviewed)

  1. Nagai, Y., Yura, K., Kagawa, H., Wako, H. (2012) Discretized Curvature Analysis for Ribose and Adenine Rings of ATP-Analogs Bound to Myosin, in Memoirs of Kokushikan University Center for Information Science, 33, 55-60.
  2. Kinoshita, K., Kono, H., Yura, K. (2008) Prediction of molecular interactions from 3D-structures: from small ligands to large protein complexes, in Prediction of Protein Structures, Functions, and Interactions (ed. Bujnicki, J.M.), Wiley and Sons,159-186.
  3. Go, M., Yura, K. (1999) Protein Folding and Genome Evolution, in "Old and New Views of Protein Folding (eds. Kuwajima, K. and Arai, M.), Elsevier, 239-248.
  4. Yura, K., Go, M. (1995) Helix-turn-helix module distribution and module shuffling, in "Tracing Biological Evolution in Protein and Gene Structures" (eds. M. Go and P. Schimmel), Elsevier, 187-196. (Google Scholar Cited by ...)
  5. Tateno, M. , Mizutani, M., Yura K., Nureki, O., Yokoyama, S., Go, M. (1995) Module structure and function of glutamyl-tRNA synthetase, in "Tracing Biological Evolution in Protein and Gene Structures" (eds. M. Go and P. Schimmel), Elsevier, 53-64.
  6. Saito, N., Yura, K. and Fukuda, Y. (1990) Some remarks on protein folding, in "Protein Structural Analysis, Folding and Design" (ed. M. Hatano), Japan Sci. Soc. Press and Elsevier, 19-35.

Publication in Japanese

  1. 由良　敬、高井美智留（分担執筆） (2013) 第4 章　タンパク質進化の機構、 「進化分子工学─高速分子進化によるタンパク質・核酸の開発─」（伏見　譲　監修）　エヌ・ティー・エス、　pp.61-70,口絵-2,口絵-3.
  2. 倭　剛久、由良　敬 (2013) 分子動力学とデータベースによる統合解析、 生化学, 85(8), 646-655.
  3. 由良　敬 (2013) 【翻訳】天然変性タンパク質、 パリティ, 28(06), 45-47.
  4. 川井優里、板垣　舞、芳須公美、竹田宏美、由良　敬 (2013) 数学・理科教育教材の開発に向けての取組み、 情報知識学会誌, 23(2), 199-204.
  5. 由良　敬 （分担翻訳） (2012) 「ヘンダーソン生物学用語辞典」 （生物学用語辞典編集員会）　オーム社.
  6. 由良　敬 (2012) 巻頭言：境界にいることを楽しもう、 生物物理, 52 (3), 123.
  7. 由良　敬 (2012) RNAの塩基配列はDNAの塩基配列と完全に一致するのか？、 生物の科学 遺伝, 66 (3), 237-239.
  8. 由良　敬 (2011) 埋め草「タンパク質立体構造散歩」の経緯、 生物物理, 51 (3), 144-145.
  9. 由良　敬（分担執筆） (2010) 「タンパク質の立体構造入門：基礎から構造バイオインフォマティクスへ」（藤博幸　編集）第１章 タンパク質構造の基礎、講談社 pp. 1-17. (本書のホームページ)
  10. 由良　敬 (2010) 「タンパク質の構造から機能を推定する：構造バイオインフォマティクス」、 化学と生物, 48(1), 43-50.
  11. 由良　敬、郷　通子 (2009) 陸上植物オルガネラのRNA編集の役割、 生物物理, 49(5), 244-245.
  12. 由良　敬、塩生真史、藤　博幸 (2009) 構造バイオインフォマティクス、 蛋白質核酸酵素 (PNE) , 増刊号『融合発展する構造生物学とケミカルバイオロジーの最前線』, 54(12), 1535-1541.
  13. 倭　剛久、西岡宏任、由良　敬 (2009) 理論計算＋生命情報学で初めて見出された活性部位の機能性残基 −ＤＮＡ補修酵素の場合―、 生物物理, 49(4), 196-197.
  14. 由良　敬 (2008) タンパク質の立体構造に基づく相互作用構造の推定、 薬学雑誌, 128 (11), 1547-1555.
  15. 由良　敬（分担執筆） (2007) 「生物物理学ハンドブック」（石渡信一、桂　勲、桐野　豊、美宅成樹　編集）1.6 ドメイン，モチーフ，モジュール　朝倉書店 pp. 51-53.
  16. 由良　敬（分担執筆） (2006) 「バイオインフォマティクス事典」（日本バイオインフォマティクス学会事典編纂）　共立出版 pp. 251-258, 601-602, 607-609.
  17. 由良　敬、山口晶太、郷　通子 (2005) 全ゲノムを対象とした蛋白質立体構造データベースの公開、 蛋白質核酸酵素増刊号「ゲノムから生命システムへ」 共立出版　50 p. 2301.
  18. 由良　敬（分担執筆） (2005) 第３章５節　ビタミン、ミネラルのかたち、 「食品の科学」（上野川修一、田之倉優　編集） 東京化学同人　 pp.87-95 .
  19. 郷　通子、由良　敬 (2005) タンパク質のフォールディング.　自己組織化と遺伝子のスプライシング 「Bionics」 オーム社　2 (1), pp. 38-43.
  20. 由良　敬（分担執筆） (2004) 第６章 データベースの構築と活用、 「基礎と演習　バイオインフォマティクス」（郷　通子、高橋健一編）　共立出版 　 pp.133-164.
  21. 由良　敬、郷　信広（分担執筆） (2003) タンパク質立体構造の進化、 「ゲノムからみた生物の多様性と進化」（五條堀孝　編集）　シュプリンガー・フェアラーク　 pp.33-40.
  22. 由良　敬 (2003) バイオインフォマティクスが追い求めるもの、 名古屋大学情報連携基盤センターニュース. 2 (2), pp. 136-143.
  23. 由良　敬 (2002) ゲノム配列にもとづくタンパク質機能予測、 「プロテオミクスの最新技術」 深見泰夫監修、シーエムシー出版 pp. 93-101.
  24. 由良　敬、郷　通子 (2002) モジュールに基づくゲノム機能予測、 蛋白質核酸酵素増刊「構造プロテオミクス」 共立出版 47,pp. 1090-1096.
  25. 由良　敬、郷　通子 (2001) POUドメイン、 「生体の科学：モチーフ・ドメインリスト」金原一郎記念医学医療振興財団／医学書院. 52 (5), pp.384-385.
  26. 由良　敬、郷　通子 (2001) ジンクフィンガードメイン、 「生体の科学：モチーフ・ドメインリスト」金原一郎記念医学医療振興財団／医学書院. 52 (5), pp.394-395.
  27. 由良　敬（分担執筆） (2000) タンパク質立体構造に基づくゲノム機能予測、 「ゲノム情報生物学−BioinformaticsとInformation Biology」（松原謙一、榊　佳之　監修）　中山書店　pp.100-115. （韓国語訳本）
  28. 郷　通子、由良　敬 (1998) 相互作用と構造ブロック、 「遺伝子の構造生物学」（嶋本伸雄、郷通子　編集）共立出版. pp. 169-179.
  29. 由良　敬、篠田和紀、井本剛史、郷　通子 (1997) DNA塩基配列を用いたfastDNAmlによる進化系統樹の推定、 名古屋大学大型計算機センターニュース. 28 (2), pp. 127-135.

Being Acknowledged

  1. Oda, Y., Yui, R., Sakamoto, K., Kita, K., Matsuura. E.T. (2012) Age-related changes in the activities of respiratory chain complexes and mitochondrial morphology in Drosophila. Mitochondrion, 12 (2), 345-351.
  2. Jansson, J., Lemence R.S., Lingas, A. (2012) The complexity of inferring a minimally resolved phylogenetic supertree. SIAM Journal on Computing, 41 (1), 272-291.
  3. Nomura, T., Kamada, R., Ito, I., Sakamoto, K., Chuman, Y., Ishimori, K., Shimohigashi, Y., Sakaguchi, K. (2011) Probing Phenylalanine Environments in Oligomeric Structures with Pentafluorophenylalanine and Cyclohexylalanine. Biopolymers, 95 (6), 410-419.
  4. Higuchi, M., Fujii, J., Yonetani, Y., Kitao, A., Go, N. (2011) Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding. Journal of Structural Biology, 173 (1), 20-28.
  5. Hayward, S., Kitao, A. (2010) The effect of end constraints on protein loop kinematics. Biophysical Journal, 98 (9), 1976-1985.
  6. Masuda, N., Kawamura, Y., Kori, H. (2009) Impact of hierachical modular structure on ranking of individual nodes in directed networks. New Journal of Physics, 11 113002 (21pp).
  7. Ishida, H., Hayward, S. (2008) Path of Nascent Polypeptide in Exit Tunnel Revealed by Molecular Dynamics Simulation of Ribosome. Biophysical Journal, 95 (12), 5962-5973.
  8. Kawabata, T. (2008) Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model. Biophysical Journal, 95 (10), 4643-4658.
  9. Kim, OTP., Sakurai, A., Saito, K., Ito, K., Ikehara, K., Harumoto, T. (2008) Ciliates use both variant and universal genetic codes: Evidence of omnipotent eRF1s in the class Litostomatea Gene, 417 (1-2), 51-58.
  10. Jin, W., Takada, S. (2008) Asymmetry in membrane protein sequence and structure: Glycine outside rule. Journal of Molecular Biology, 337 (1), 74-82.
  11. Nakahara, T., Hashimoto, R., Nakagawa, H., Monde, K., Miura, N., Nishimura, S. (2008) Glycoconjugate Data Bank:Structures - an annotated glycan structure database and N-glycan primary structure verification service. Nucleic Acids Research, 36, D368-D371 (open access).
  12. Fukuhara, N., Go, N., Kawabata, T. (2007) Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. BIOPHYSICS, 3, 13-26 (open access).
  13. Yonetani, Y. (2006) Liquid water simulation: A critical examination of cutoff length. J. Chem. Phys., 124 (20), 204501.
  14. Iwaoka, M., Isozumi, N. (2006) Possible roles of S...O and S...N interactions in the functions and evolution of phospholipase A2. BIOPHYSICS, 2, 23-34 (open access).
  15. Go, M., Schimmel, P., Morishima, I., Wakasugi, K., Takada, S., Peng, Z., Arai, M. (2001) Memories of TANIGUCHI International Symposium Seibutsu Butsuri, 41 (1), 42-47 (open access).
  16. Yamaguchi-Kabata, Y., Gojobori, Y. (2000) Reevaluation of Amino Acid Variability of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein and Prediction of New Discontinuous Epitopes. Journal of Virology, 74 (9), 4335-4350 (open access).
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