Publication List of Ken Nishikawa
Review articles
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Nishikawa, K., “Tertiary structure of proteins: Representation and conformational analysis”, Dissertation, Kyoto Univ. (1972).
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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).
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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).
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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).
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Nishikawa, K. “Protein structure prediction”, in The Encyclopedia of Molecular Biology (Ed., T.E. Creighton), John Wiley & Sons, Inc. (1999).
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Nishikawa, K. “Editorial: Information concept in biology”, Bioinformatics, 18, 649-651 (2002).
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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
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Nishikawa, K., Oobatake, M. & Ooi, T., “Tertiary structure of proteins: Analysis of conformations”, Bull. Inst. Chem. Res., Kyoto Univ., 48, 102-110 (1970).
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Nishikawa, K. & Ooi, T., “Rotational freedom in proline residue”, Prog. Theor. Phys., 46, 670-671 (1971).
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Nishikawa, K. & Ooi, T., “Energy calculations on di- and poly-L-proline”, Bull. Inst. Chem. Res., Kyoto Univ., 50, 94-106 (1972).
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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).
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Nishikawa, K. & Ooi, T., “Tertiary structure of proteins . II. Freedom of dihedral angles and energy calculation”, J. Phys. Soc. Japan, 32, 1338-1347 (1972).
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Mattice, W.L., Nishikawa, K. & Ooi, T., “Conformational properties of poly(L-proline )containing a flexible pyrrolidine ring”, Macromolecules, 6, 443-446 (1973)
- Nishikawa, K. & Ooi, T., “Comparison of homologous tertiary structure of proteins", J. Theor. Biol., 43, 351-374 (1974).
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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).
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Nishikawa, K. & Scheraga, H.A., “Geometrical criteria for formation of coiled-coil structures of polypeptide chains”, Macromolecules, 9, 395-407 (1976).
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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).
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Ooi, T. & Nishikawa, K., “Utilization of computer for determination of a nucleotide sequence”, Bull. Inst. Chem. Res., Kyoto Univ., 56, 93-100 (1978).
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Nishikawa, K. & Ooi, T., “Chain dimension and effective potential energy of globular proteins”, Macromolecules, 11, 644-647 (1978).
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Ooi, T., Nishikawa, K., Oobatake, M. & Scheraga, H.A., “Flexibility of bovine pancreatic trypsin inhibitor”, Biochim. Biophys. Acta, 536, 390-405 (1978).
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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).
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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).
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Ooi, T. & Nishikawa, K., “Energy surface of protein molecule in the conformational phase space”, J. Phys. Soc. Japan, 50, 261-269 (1981).
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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).
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Kubota, Y., Takahashi, S., Nishikawa, K. & Ooi, T., “Homology in protein sequences expressed by correlation coefficients”, J. Theor. Biol., 91, 347-361 (1981).
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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).
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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). -
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
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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).
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Nishikawa, K., “Assessment of secondary-structure prediction of proteins: Comparison of computerized Chou-Fasman method with others”, Biochim. Biophys. Acta, 748, 285-299 (1983).
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Nishikawa, K., “Solvent effects on a protein molecule: A theoretical inspection”, Bull. Inst. Chem. Res., Kyoto Univ., 61, 247-264 (1983).
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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).
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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).
- 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).
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Nishikawa, K. & Ooi, T., “Radial locations of amino acid residues in a globular protein: Correlation with the sequence”, J. Biochem., 100, 1043-1047 (1986).
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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).
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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).
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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).
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Konishi, Y. & Nishikawa, K., “A highly reliable prediction of protein secondary structure”, Bull. Inst. Chem. Res., Kyoto Univ., 66, 378-385 (1989).
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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).
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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).
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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).
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von Heijne, G. & Nishikawa, K., “Chloroplast transit peptides: The perfect random coil?”, FEBS Lett., 78, 1-3 (1991).
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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).
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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).
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Nishikawa, K. & Noguchi, T., “Predicting protein secondary structure based on amino acid sequence”, Meth. Enzymol., 202, 31-44 (1991).
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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).
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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).
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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)
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Nishikawa, K., "Island hypothesis: Protein distribution in the sequence space", Viva Origino 21, 91-102 (1993)
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Nishikawa, K. & Matsuo, Y., "Development of pseudoenergy potentials for assessing protein 3D-1D compatibility and detecting weak homologies", Prot. Engineer. 6, 811-820 (1993)
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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).
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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)
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Nishikawa, K., Ishino, S., Takenaka, H., Norioka, N., Hirai, T., Yao, T. & Seto, Y., "Constructing a protein mutant database", Protein Engineer., 7, 733 (1994)
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Matsuo, Y. & Nishikawa, K., "Prediction of the structural similarity between spermidine/putrescine-binding protein and maltose-binding protein", FEBS Lett., 345, 23-26 (1994)
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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)
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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)
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Matsuo, Y. & Nishikawa, K., "Protein structural similarities predicted by a sequence-structure compatibility method", Protein Sci., 3, 2055-2063 (1994)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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).
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Suyama, M., Matsuo, Y. & Nishikawa, K., "Comparison of protein structures using 3D profile alignment", J. Mol. Evol., 44 (Suppl 1) S163-S173 (1997)
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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)
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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)
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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)
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Ito, M., Matsuo, Y. & Nishikawa, K., “Prediction of protein secondary structure using the 3D-1D compatibility algorithm”, CABIOS, 13, 415-423 (1997)
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Nakashima, H., Nishikawa, K. & Ooi, T., “Differences in dinucleotide frequencies of human, yeast, and E. coli genes”, DNA Res. 4, 185-192 (1997)
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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)
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Ota, M., Isogai, Y. & Nishikawa, K. “Structural requirement of highly-conserved residues in globins”, FEBS Lett., 415, 129-133 (1997)
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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)
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Kawabata, T., Ota, M. & Nishikawa, K., “The Protein Mutant Database”, Nucl. Acids Res., 27, 355-357 (1999)
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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)
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Ota, M. & Nishikawa, K. “Feasibility in the inverse protein folding protocol”, Protein Sci. 8, 1001-1009 (1999)
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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)
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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)
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Nagano, N., Ota, M. & Nishikawa, K. “Strong hydrophobic nature of cysteine residues in proteins”, FEBS Lett., 458, 69-71 (1999)
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Ota, M., Kawabata, T., Kinjo, A.R. & Nishikawa, K. “Cooperative approach for the protein fold recognition”, PROTEINS, Suppl. 3, 126-132 (1999)
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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).
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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).
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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).
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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).
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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).
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Kawabata, T. & Nishikawa, K. “Protein structure comparison using the Markov transition matrix of evolution”, PROTEINS, 41, 108-122 (2000).
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Kawabata, T., Arisaka, F. & Nishikawa, K. “Structural/functional assignment of bacteriophage T4 unknown proteins by iterative database searches”, GENE, 259, 223-233 (2000).
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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)
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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).
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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).
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Kinjo, R.A. and Nishikawa, K., “Comparison of energy components of proteins from thermophilic and mesophilic organisms”, Eur. Biophys. J., 30, 378-384 (2001).
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Fukuchi, S. and Nishikawa, K., “Protein surface amino-acid composition distinctively differ between thermophilic and mesophilic bacteria”, J. Mol. Biol., 309, 835-843 (2001).
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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).
- 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).
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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).
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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).
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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). -
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).
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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)
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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).
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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).
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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).
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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).
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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).
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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).
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Fukuchi, S. and Nishikawa, K., “Estimation of the number of authentic orphan genes in bacterial genomes”, DNA Res., 11, 219-231 (2004).
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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).
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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).
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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).
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Kinjo, A.R. and Nishikawa, K., “Recoverable one-dimensional encoding of three-dimensional protein structures”, Bioinformatics, 21(10), 2167-2170 (2005)
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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).
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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).
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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)
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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)
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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)
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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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Fukuchi, S., Homma, K., Sakamoto, S., Sugawara, H., Tateno, Y., Gojobori, T. and Nishikawa, K. “The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions”, Nucl. Acids Res. 37, D333-D337 (2009)
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