蛋白質立体構造の二次元マップ表示

３名の共著者の方々のご承諾を得て、この論文と同じ内容を博士論文（和文）にまとめ、理学博士号を取得した（西川建、1972）。

発表論文リスト

Publication List of Ken Nishikawa

Review articles 

1. Nishikawa, K., “Tertiary structure of proteins: Representation and conformational analysis”, Dissertation, Kyoto Univ. (1972).

2. Ooi, T. & Nishikawa, K., “One approach to computing the tertiary structure of proteins”, in Conformation of Biological Molecules and Polymers, The Jerusalem Symposia on Quantum Chemistry and Biochemistry, Vol. 5, pp. 173-187 (1973).

3. Nishikawa, K., Noguchi, T. & Konishi, Y. “Highly reliable secondary-structure prediction of proteins by a new joint method”, Protein Engineering: Protein Design in Basic Research, Medicine, and Industry} (ed. Ikehara, M.) Japan Scientific Societies Press, Sprenger-Verlag, 29-34 (1990).

4. Nishikawa, K., Iwama, H. & Saito, N., “Prediction of tertiary structure of protein by folding simulation using hydrophobic interaction”, Computer Aided Innovation of New Materials II, (Eds., Doyama et al.) Elsevier Science Publishers B.V., pp. 1271-1274 (1993).

5. Nishikawa, K. “Protein structure prediction”, in The Encyclopedia of Molecular Biology (Ed., T.E. Creighton), John Wiley & Sons, Inc. (1999).

6. Nishikawa, K. “Editorial: Information concept in biology”, Bioinformatics, 18, 649-651 (2002).

7. Fukuchi, S., Homma, K., Sakamoto, S. and Nishikawa, K., “GTOP:http://spock.genes.nig.ac.jp/~genome/gtop.html” Online Journal of Nucleic
   Acids Research (2003)　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　          

Original papers

1. Nishikawa, K., Oobatake, M. & Ooi, T., “Tertiary structure of proteins: Analysis of conformations”, Bull. Inst. Chem. Res., Kyoto Univ., 48, 102-110 (1970).

2. Nishikawa, K. & Ooi, T., “Rotational freedom in proline residue”, Prog. Theor. Phys., 46, 670-671 (1971).

3. Nishikawa, K. & Ooi, T., “Energy calculations on di- and poly-L-proline”, Bull. Inst. Chem. Res., Kyoto Univ., 50, 94-106 (1972).

4. Nishikawa, K., Ooi, T., Isogai, Y. & Saito, N., “Tertiary structure of proteins . I. Representation and computation of the conformations”, J. Phys. Soc. Japan, 32, 1331-1337 (1972).

5. Nishikawa, K. & Ooi, T., “Tertiary structure of proteins . II. Freedom of dihedral angles and energy calculation”, J. Phys. Soc. Japan, 32, 1338-1347 (1972).　　　　

6. Mattice, W.L., Nishikawa, K. & Ooi, T., “Conformational properties of poly(L-proline )containing a flexible pyrrolidine ring”, Macromolecules,  6, 443-446 (1973)

7. Nishikawa, K. & Ooi, T., “Comparison of homologous tertiary structure of proteins",  J. Theor. Biol., 43, 351-374 (1974).

8. Nishikawa, K., Momany, F.A. & Scheraga, H.A., “Low-energy structures of two dipeptides and their relationship to bend conformations”, Macromolecules, 7, 797-806 (1974).

9. Nishikawa, K. & Scheraga, H.A., “Geometrical criteria for formation of coiled-coil structures of polypeptide chains”, Macromolecules, 9, 395-407 (1976).

10. Kontani, T., Nishikawa, K., Iio, T., Takahashi, S. & Ooi, T., “Unidirectional stability of $¥alpha$-helix. Theoretical calculation and attempt for synthesis of block copolypeptides”, Bull. Inst. Chem. Res., Kyoto Univ., 54, 128-140 (1976).

11. Ooi, T. & Nishikawa, K., “Utilization of computer for determination of a nucleotide sequence”, Bull. Inst. Chem. Res., Kyoto Univ., 56, 93-100 (1978).

12. Nishikawa, K. & Ooi, T., “Chain dimension and effective potential energy of globular proteins”, Macromolecules, 11, 644-647 (1978).

13. Ooi, T., Nishikawa, K., Oobatake, M. & Scheraga, H.A., “Flexibility of bovine pancreatic trypsin inhibitor”, Biochim. Biophys. Acta, 536, 390-405 (1978).

14. Nishikawa, K. & Ooi, T., “Prediction of the surface-interior diagram of globular proteins by an empirical method”, Int. J. Peptide Protein Res., 16, 19-32 (1980).

15. Nishikawa, K., Oobatake, M. & Ooi, T., “Method for energy computation of protein structures. A set of amino acid geometries and energy parameters”, Bull. Inst. Chem. Res., Kyoto Univ., 58, 308-322 (1980).

16. Ooi, T. & Nishikawa, K., “Energy surface of protein molecule in the conformational phase space”, J. Phys. Soc. Japan, 50, 261-269 (1981).

17. Noguchi, T., Go, N., Ooi, T. & Nishikawa, K., “Monte Calro simulation study of thermal fluctuations and conformational energy surface of a small protein, basic pancreatic trypsin inhibitor”, Biochim. Biophys. Acta, 671, 93-98 (1981).

18. Kubota, Y., Takahashi, S., Nishikawa, K. & Ooi, T., “Homology in protein sequences expressed by correlation coefficients”, J. Theor. Biol., 91, 347-361 (1981).

19. Kubota, Y., Nishikawa, K., Takahashi, S. & Ooi, T., “Correspondence of homologies in amino acid sequence and tertiary structure of protein molecules”, Biochim. Biophys. Acta, 701, 242-252 (1982).

20. Nishikawa, K. & Ooi, T., “Correlation of the amino acid composition of a protein to its structural and biological character”, J. Biochem., 91, 1821-1824
    (1982).

21. Nishikawa, K., Kubota, Y. & Ooi, T., “Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution”, J. Biochem., 94, 981-995 

22. Nishikawa, K., Kubota, Y. & Ooi, T., “Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types”, J. Biochem., 94, 997-1007 (1983).

23. Nishikawa, K., “Assessment of secondary-structure prediction of proteins: Comparison of computerized Chou-Fasman method with others”, Biochim. Biophys. Acta, 748, 285-299 (1983). 

24. Nishikawa, K., “Solvent effects on a protein molecule: A theoretical inspection”, Bull. Inst. Chem. Res., Kyoto Univ., 61, 247-264 (1983).

25. Ishijima, S., Katagiri, F., Kodaki, T., Izui, K., Katsuki, H., Nishikawa, K., Nakashima, H. & Ooi, T., “Comparison of amino acid sequences between Phosphoenolpyruvate carboxylases from Escherichia coli (allosteric) and Anacystis nidulans (non-allosteric): Identification of conserved and variable regions”, Biochem. Biophys. Res. Commun., 133, 436-441 (1985).

26. Nakashima, H., Nishikawa, K. & Ooi, T., “The folding type of a protein is relevant to the amino acid composition”, J. Biochem., 99, 153-162 (1986).

27. Nishikawa, K. & Ooi. T., “Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods”, Biochim. Biophys. Acta, 871, 45-54 (1986). 

28. Nishikawa, K. & Ooi, T., “Radial locations of amino acid residues in a globular protein: Correlation with the sequence”, J. Biochem., 100, 1043-1047 (1986).

29. Matsukage, A., Nishikawa, K., Ooi,T., Seto, Y. & Yamaguchi, M., Homology between mammalian DNA polymerase beta and terminal deoxynucleotidyl transferase”, J. Biol. Chem., 262, 8960-8962 (1987).

30. Nishikawa, K., Nakashima, H., Kanehisa, M. & Ooi, T., “Detection of weak sequence homology of proteins for tertiary structure prediction”, Prot. Seq. Data Anal., 1, 107-116 (1987).

31. Nakashima, H., Nishikawa, K. & Ooi, T., “Segmentation of a protein into structural elements: Analysis and classification of segments”, J. Protein Chem., 7, 509-525 (1988).

32. Konishi, Y. & Nishikawa, K., “A highly reliable prediction of protein secondary structure”, Bull. Inst. Chem. Res., Kyoto Univ., 66, 378-385 (1989).

33. Fujimoto, T., Takahashi, H., Kubota, Y., Nakashima, H. & Nishikawa, K., “A system for protein sequence analysis constructed on workstation”, Bull. Inst. Chem. Res., Kyoto Univ., 66, 386-397 (1989).

34. Suzuki, H., Kawarabayashi, Y., Kondo, J., Abe, T., Nishikawa, K., Kimura, S., Hashimoto, T. & Yamamoto, T., “Structure and regulation of rat long-chain acyl-CoA synthetase”, J. Biol. Chem., 265, 8681-8685 (1990).

35. Nakashima, H., Nishikawa, K. & Ooi, T., “Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins”, Proteins: Str. Func. Gen., 8, 173-178 (1990).

36. von Heijne, G. & Nishikawa, K., “Chloroplast transit peptides: The perfect random coil?”, FEBS Lett., 78, 1-3 (1991).

37. Tamura, H., Kohchi, C., Yamada, R., Ikeda, T., Koiwai, O., Patterson, E., Keene J.D., Okada, K., Kjeldsen, E., Nishikawa, K. & Andoh, T., “Molecular cloning of a cDNA of a camptothecin-resistant human DNA topoisomerase I and identification of mutation sites”, Nucl. Acid. Res., 19, 69-75 (1991).

38. Hattori, T., Shiozaka, K., Eda, Y., Tokiyoshi, S., Matsushita, S., Inaba, H., Fujimaki, M., Meguro, T., Yamada, K., Honda, M., Nishikawa, K. & Takatsuki, K., “Characteristics of the principal neutralizing determinant of HIV-1 prevalent in Japan”, Human Retrovirus AIDS Res., 7, 825-830 (1991).

39. Nishikawa, K. & Noguchi, T., “Predicting protein secondary structure based on amino acid sequence”, Meth. Enzymol., 202, 31-44 (1991).

40. Nakashima, H. & Nishikawa, K., “The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins”, FEBS Lett., 303, 141-146 (1992). 

41. Nakashima, H., Nishikawa, K. & Ooi, T., “E. coli proteins with eukaryotic homologues sitting in series on the bacterial genome”, J. Prot. Chem., 11, 392-393 (1992).

42. Saitoh, S., Nakai, T. & Nishikawa, K., "A geometrical constraint approach for reproducing the native backbone conformation of a protein", Proteins: Str. Func. Genet., 15, 191-204 (1993)

43. Nishikawa, K., "Island hypothesis: Protein distribution in the sequence space", Viva Origino 21, 91-102 (1993) 

44. Nishikawa, K. & Matsuo, Y., "Development of pseudoenergy potentials for assessing protein 3D-1D compatibility and detecting weak homologies", Prot. Engineer. 6, 811-820 (1993)

45. Mitsui, H., Yamaguchi-Shinozaki, K., Shinozaki, K., Nishikawa, K. & Takahashi, H., “Identification of a gene family (kat) encoding kinesin-like proteins in Arabidopsis thaliana and the characterization of secondary structure of KatA”, Mol. Gen. Genet., 238, 362-368 (1993).

46. Nakashima, H. & Nishikawa, K., "Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies", J. Mol. Biol., 238, 54-61 (1994)

47. Nishikawa, K., Ishino, S., Takenaka, H., Norioka, N., Hirai, T., Yao, T. & Seto, Y., "Constructing a protein mutant database", Protein Engineer., 7, 733 (1994)

48. Matsuo, Y. & Nishikawa, K., "Prediction of the structural similarity between spermidine/putrescine-binding protein and maltose-binding protein", FEBS Lett., 345, 23-26 (1994)

49. Amano, T., Yoshida, M., Matsuo, Y. & Nishikawa, K., "Structural model of the ATP-binding domain of the F1-beta subunit based on analogy to the RecA protein", FEBS Lett. 351, 1-5 (1994)

50. Mitsui, H., Nakatani, K., Yamaguchi-Shinozaki, K., Shinozaki, K., Nishikawa, K. & Takahashi, H., "Sequencing and characterization of the kinesin-related genes katB and katC of Arabidopsis thaliana", Plant Mol. Biol., 25, 865-876 (1994)

51. Matsuo, Y. & Nishikawa, K., "Protein structural similarities predicted by a sequence-structure compatibility method", Protein Sci., 3, 2055-2063 (1994)

52. Shiraki, K., Nishikawa, K. & Goto, Y., "Trifluoroethanol-induced stabilization of the -helical structure of -lactoglobulin: Implication for non-hierarchical protein folding", J. Mol. Biol. 245, 180-194 (1995)

53. Tabish, M., Siddiqui, Z.K., Nishikawa, K. & Siddiqui, S.S., "Exclusive expression of C. elegans osm-3 kinesin gene in chemosensory neurons open to the external environment", J. Mol. Biol., 247, 377-389 (1995)

54. Matsunaga, F., Kawasaki, Y., Ishiai, M., Nishikawa, K., Yura, T. & Wada, C., "DNA-binding domain of the repE initiator protein of mini-F plasmid: Involvement of the carboxyl-terminal region", J. Bacteriol., 177, 1994-2001 (1995)

55. Ota, M., Kanaya, S. & Nishikawa, K., "Desk top analysis of the structural stability of various point mutations introduced into ribonuclease H", J. Mol. Biol. 248, 733-738 (1995)

56. Matsuo, Y., Nakamura, H. & Nishikawa, K., "Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions", J. Biochem. 118, 137-148 (1995)

57.  Ikezawa, H., Tameishi, K., Yamada, A., Tamura, H., Tsukamoto, K., Matsuo, Y. & Nishikawa, K., "Studies on the active sites of Bacillus cereus shpingomyelinase substitution of some amino acids by site-directed mutagenesis", Amino Acids, 9, 293-298 (1995)

58.  Tamura, H., Tameishi, K., Yamada, A., Tomita, M., Matsuo, Y., Nishikawa, K. & Ikezawa, H., "Mutation in aspartic acid residues modifies catalytic and haemolytic activities of Bacillus cereus sphingomyelinase", Bochem. J. 309, 757-764 (1995)

59.  Matsuo, Y. & Nishikawa, K., "Assessment of a protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding, and local conformation", Proteins: Str. Func. Genet., 23, 370-375 (1995)

60.  Kido, S., Doi, Y., Kim, F., Morishita, E., Narita, H., Kanaya, S., Ohkubo, T., Nishikawa, K., Yao, T. & Ooi, T., “Characterization of vitelline membrane outer layer protein I, VMO-I: amino acid sequence and structural stability”, J.Biochem. (tokyo), 117, 1183-1191 (1995)

61.  Matsuo, Y., Yamada, A., Tsukamoto, K., Tamura, H., Ikezawa, H., Nakamura, H.& Nishikawa, K., "A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I", Prot. Sci., 5, 2459-2467 (1996).

62.  Suyama, M., Matsuo, Y. & Nishikawa, K., "Comparison of protein structures using 3D profile alignment", J. Mol. Evol., 44 (Suppl 1) S163-S173 (1997)

63.  Ota, M. & Nishikawa, K., ``Assessment of the pseudo-energy potential by the best-five test: a new use of the three-dimensional profiles of proteins'', Prot. Eng. 10, 339-351 (1997)

64.  Gready, J.E., Ranganathan, S., Schofield, P.R., Matsuo, Y. & Nishikawa, K., “Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand binding site”,Prot. Sci., 6, 983-998 (1997)

65.  Sumikawa, H., Fukuhara, K., Suzuki, E., Matsuo, Y. & Nishikawa, K., “Tertiary structural models for human interleukin-6 and evaluation by a sequence-structure compatibility method and NMR experimental information”, FEBS Lett. 404, 234-240 (1997)

66.  Ito, M., Matsuo, Y. & Nishikawa, K., “Prediction of protein secondary structure using the 3D-1D compatibility algorithm”, CABIOS, 13, 415-423 (1997)

67.  Nakashima, H., Nishikawa, K. & Ooi, T., “Differences in dinucleotide frequencies of human, yeast, and E. coli genes”, DNA Res. 4, 185-192 (1997)

68.  Khan, M.L.A., Gogonea, C.B., Siddiqui, Z.K., Ali, M.Y., Kikuno, R., Nishikawa, K. & Siddiqui, S.S., “Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd”, J. Mol. Biol., 270, 627-639 (1997)

69.  Ota, M., Isogai, Y. & Nishikawa, K. “Structural requirement of highly-conserved residues in globins”, FEBS Lett., 415, 129-133 (1997)

70.  Nakashima, H., Ota, M., Nishikawa, K. & Ooi, T., “Genes from nine genomes are separated into their organisms in the dinucleotide composition space”, DNA Res., 5, 251-259 (1998)

71.  Kawabata, T., Ota, M. & Nishikawa, K., “The Protein Mutant Database”, Nucl. Acids Res., 27, 355-357 (1999)

    72.  

72. Fukami-Kobayashi, K., Tateno, Y. & Nishikawa, K., “Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history”, J. Mol. Biol., 286, 279-290 (1999) 

73. Ota, M. & Nishikawa, K. “Feasibility in the inverse protein folding protocol”, Protein Sci. 8, 1001-1009 (1999)

74. Isogai, Y., Ota, M., Fujisawa, T., Izuno, H., Mukai, M., Nakamura, H., Iizuka, T. & Nishikawa, K. “Design and synthesis of a globin fold”, Biochemistry, 38, 7431-7443 (1999)

75. Takano, K., Ota, M., Ogasahara, K., Yamagata, Y., Nishikawa, K. & Yutani, K. Experimental Verification of Table for "Stability Profile of Mutant Protein" (SPMP) Using Mutant Human Lysozymes, Protein Engng., 12, 663-672 (1999)

76. Nagano, N., Ota, M. & Nishikawa, K. “Strong hydrophobic nature of cysteine residues in proteins”, FEBS Lett., 458, 69-71 (1999) 

77. Ota, M., Kawabata, T., Kinjo, A.R. & Nishikawa, K. “Cooperative approach for the protein fold recognition”, PROTEINS, Suppl. 3, 126-132 (1999)

78. Yusuf Ali, M., Khan, M.L.A., Shakir, M.A., Fukami-Kobayashi,K., Nishikawa, K. & Siddiqui, S.S., “Expression and cDNA cloning of klp-12 gene encoding an ortholog of the chicken chromokinesin, mediating chromosome segregation in C. elegans”, J. Biochem. Mol. Biol., 33, 138-146 (2000).

79. Khan, M.L.A., Yusuf Ali, M., Siddiqui, Z.K., Shakir, M.A., Ohnishi, H., Nishikawa, K. & Siddiqui, S.S. “C. elegans KLP-11/OSM-3/KAP-1: Orthologs of the sea urchin kinesin-II, and mouse KIF3A/KIFB/KAP3 kinesin complexes”, DNA Res., 7, 121-125 (2000).

80. Isogai, Y., Ishii, A., Fujisawa, T., Ota, M. & Nishikawa, K. “Redesign of artificial globins: Effects of residue replacements at hydrophobic sites on the structural properties”, Biochemistry, 39, 5683-5690 (2000).

81. Nakashima, H. & Nishikawa, K., “The genomic DNA sequences of various species are distinctively distributed in nucleotide composition space”, Res. Comm. In Biochem., Cell & Mol. Biol., 4, 25-45 (2000).

82. Isogai, Y., Ishii, A., Ishida, M., Mukai, M., Ota., M., Nishikawa, K. & Iizuka, T. “Structural and functional properties of designed globins”, Proc. Indian Acad. Sci. (Chem. Sci.), 112, 215-221 (2000).

83. Kawabata, T. & Nishikawa, K. “Protein structure comparison using the Markov transition matrix of evolution”, PROTEINS, 41, 108-122 (2000).

84. Kawabata, T., Arisaka, F. & Nishikawa, K. “Structural/functional assignment of bacteriophage T4 unknown proteins by iterative database searches”, GENE, 259, 223-233 (2000).

85. Kinjo, A.R., Kidera, A., Nakamura, H. & Nishikawa, K. “Physico-chemical evaluation of protein folds predicted by threading”, Eur. Biophys. J., 30, 1-10 (2001)

86. Nakashima, H., Yamashita, S. and Nishikawa, K., “Directional gene distributions of two mycoplasma species exhibited in the nucleotide composition space”, Res. Comm. In Biochem., Cell & Mol. Biol., 5, 27-35 (2001).

87. Noguchi, T., Ito, M., Matsuda, H., Akiyama, Y. and Nishikawa, K. “Prediction of protein secondary structure using the threading algorithm and local sequence similarity”, Res. Comm. In Biochem., Cell & Mol. Biol., 5, 115-131 (2001).

88. Kinjo, R.A. and Nishikawa, K., “Comparison of energy components of proteins from thermophilic and mesophilic organisms”, Eur. Biophys. J., 30, 378-384 (2001).

89. Fukuchi, S. and Nishikawa, K., “Protein surface amino-acid composition distinctively differ between thermophilic and mesophilic bacteria”, J. Mol. Biol., 309, 835-843 (2001).

90. Ota, M., Isogai, Y. and Nishikawa, K., “Knowledge-based potential defined for a rotamer library to design protein sequences”, Prot. Engineer., 14, 557-564 (2001).

91. Kawabata, T., Fukuchi, S., Homma, K., Ota, M., Araki, J., Ito, T., Ichiyoshi, N. and Nishikawa, K., “GTOP: A database of protein structures predicted from genome sequences”, Nucl. Acids Res., 30, 294-298 (2002).

92. Fujishima, H., Nishimura, A., Wachi, M., Takagi, H., Hirasawa, T., Teraoka, H.,

    Nishimori, K., Kawabata, T., Nishikawa, K and Nagai, K., “kdsA mutations affect FtsZ-ring formation in Escherichia coli K-12”, Microbiology, 148, 103-112 (2002).

93. Isogai, Y., Ota, M., Ishii, A., Ishida, M. and Nishikawa, K., “Identification of amino acids involved in protein structural uniqueness: Implication for de novo protein design”, Prot. Engineer., 15, 555-560 (2002).

94. Homma, K., Fukuchi, S., Kawabata, T., Ota, M. and Nishikawa, K.,
    “A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome”, Gene, 294, 25-33 (2002). 

95. Fukami-Kobayashi, K., Tateno, Y. and Nishikawa, K., “Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins”, Molecular Biology and Evolution, 20, 267-277 (2003).

96. Kashiwagi, K., Shiba, K., Fukami-Kobayashi, K., Noda, T., Nishikawa, K. and Noguchi, H. “Characterization of folding pathways of the type-1 and type-2 periplasmic binding proteins MglB and ArgT”, J. Biochem. 133, 371-376. (2003)

97. Fukuchi, S., Yoshimune, K., Wakayama, M., Moriguchi, M. and Nishikawa, K., “Unique amino acid composition of proteins in halophilic bacteria”, J. Mol. Biol., 327, 347-357 (2003). 

98. Nakashima, H., Fukuchi, S. and Nishikawa, K., “Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures”, J. Biochem., 133, 507-513 (2003). 

99. Ota, M., Kinoshita, K. and Nishikawa, K., “Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation”, J. Mol. Biol., 327, 1053-1064 (2003).

100.  Imanishi, T., Itoh, T. et al., “Integrative annotation of 21,037 human genes validated by full-length cDNA clones”, PLoS Biology 2(6): 856-875. (2004).

101. Kinjo, A.R. and Nishikawa, K., “Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins”, Bioinformatics, 20 (16) 2504-2508 (2004).

102.  Kashiwagi, K., Fukami-Kobayashi, K., Shiba, K. and Nishikawa, K. “Construction and characterization of chimeric proteins composed of type-1 and type-2 periplasmic binding proteins MglB and ArgT”, Biosci. Biotechnol. Biochem., 68 (4) 808-813 (2004).

103.  Fukuchi, S. and Nishikawa, K., “Estimation of the number of authentic orphan genes in bacterial genomes”, DNA Res., 11, 219-231 (2004).

104.  Homma, K., Kikuno, R.F., Nagase, T., Ohara, O. and Nishikawa, K., “Alternative splice variants encoding unstable protein domains exist in the human brain”, J. Mol. Biol., 343, 1207-1220 (2004).

105.  Kinjo, A.R., Horimoto, K. and Nishikawa, K., “Predicting absolute contact numbers of native protein structure from amino acid sequence”, Proteins, 58, 158-165 (2005).

106.  Saka, K., Tadenuma, M., Nakade, S., Tanaka, N., Sugawara, H., Nishikawa, K., Ichiyoshi, N.,Kitagawa, M., Mori, H., Ogasawara, N. and Nishimura, A., “A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies”, DNA Res., 12, 63-68 (2005).

107.  Kinjo, A.R. and Nishikawa, K., “Recoverable one-dimensional encoding of three-dimensional protein structures”, Bioinformatics, 21(10), 2167-2170 (2005)

108.  Minezaki, Y., Homma, K. and Nishikawa, K. “Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea”, DNA Res., 12, 269-280 (2005).

109.  Kinjo, A.R. and Nishikawa, K., “Predicting secondary structures, contact numbers and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks”, Biophysics, 1, 67-74 (2005).

110.  Fukuchi, S., Homma, K., Minezaki, Y. and Nishikawa, K., “Intrinsically disordered loops inserted into the structural domains of human proteins”, J. Mol. Biol. 355, 845-857 (2006)

111.  Ohta, T., Kawabata, T., Nishikawa, K., Tani, A., Kimbara, K. and Kawai, F., “Analysis of amino acid residues involved in the catalysis of polyethylene glycol dehydrogenase from Sphingomonas terrae using three-dimensional molecular modeling-based kinetic characterization of mutants”, Appl. Environ. Microbiol., 72, 4388-4396 (2006).

112.  Minezaki, Y., Homma, K., Kinjo, A.R. and Nishikawa, K., “Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation”, JMB, 359, 1137-1149 (2006).

113.  Haruki, M., Saito, Y., Ota, M., Nishikawa, K. and Kanaya, S., “Stabilization of E. coli ribonuclease HI by the ‘stability profile of mutant protein’ (SPMP)-inspired random and non-random mutagenesis”, J. Biotech., 124, 512-522 (2006).

114.  Kinjo, A.R. and Nishikawa, K., “CRNPRED: Highly accurate prediction of one-dimensional protein structure by large-scale Critical Random Networks”, BMC Bioinformatics, 7, 401 (2006).

115.  Homma, K., Fukuchi, S., Nakamura, Y., Gojobori, T. and Nishikawa, K., “Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in eight species of gamma-proteobacteria”, Molecular Biology and Evolution”, 24(3), 805-813, (2007).

116.  Minezaki, Y., Homma, K., and Nishikawa, K., “Intrinsically disordered regions of human plasma membrane proteins preferentially occur in the cytoplasmic segment”, J. Mol. Biol., 368(3), 902-913 (2007).

117.  Fukami-Kobayashi, K., Minezaki, Y., Tateno, Y. and Nishikawa, K., “A tree of life based on protein domain organizations”, Molecular Biology and Evolution, 24(5), 1181-1189 (2007).

118.  Nagashima, T., Kinjo, A.R., Mitsui, T. and Nishikawa, K., “Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins”, Physical Review E, 75, 066706 (2007)

119.  You, D-J., Fukuchi, S., Nishikawa, K., Koga, Y., Takano, K. and Kanaya, S., “Protein thermostabilization requires a fine-tuned placement of surface charged residues”. J. Biochem. 142, 507-516 (2007)

120.  Yamasaki, C. et al. “The H-Invitational database (H-InvDB), a comprehensive annotation resource for human genes and transcript”, Nucl. Acids Res. 36, D793-D799 (2008)

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