■■■ PUBLICATIONS ■■■

2006 2005 2004 2003 2002 2001 2000 1999

2006

Minezaki Y, Homma K, Kinjo AR, Nishikawa K.
Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J Mol Biol. 2006 Jun 16;359(4):1137-49. Epub 2006 Apr 25.

Minezaki Y, Homma K, Nishikawa K.
Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea. DNA Res. 2005;12(5):269-80. Epub 2006 Jan 10.

Fukuchi, S., Homma, K., Minezaki, Y. and Nishikawa, K.
Intrinsically disordered loops inserted into the structural domains of human proteins. J Mol Biol. 2006 Jan 27;355(4):845-57. Epub 2005 Nov 8.

2005

Kinjo, A.R., Horimoto, K. and Nishikawa, K.
Predicting absolute contact numbers of native protein structure from amino acid sequence. Proteins. 2005 Jan 1; 58(1):158-165.

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. 2005 Feb 28;12(1):63-8.

Kinjo, A.R. and Nishikawa, K.
Recoverable one-dimensional encoding of three-dimensional protein structures. Bioinformatics. 2005 May 15;21(10):2167-70. Epub 2005 Feb 18.

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).

Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T.
Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene. 2005 Dec 30;364:99-107. Epub 2005 Sep 26.

2004

Kinjo AR, 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)

Fukuchi S, Nishikawa K.
Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 2004 Aug 31;11(4):219-31, 311-313.

Homma K, Kikuno RF, Nagase T, Ohara O, Nishikawa K.
Alternative Splice Variants Encoding Unstable Protein Domains Exist in the Human Brain. J Mol Biol. 2004 Nov 5;343(5):1207-1220.

Kashiwagi K, Fukami-Kobayashi K, Shiba K, Nishikawa K.
Construction and Characterization of Chimeric Proteins Composed of Type-1 and Type-2 Periplasmic Binding Proteins MglB and ArgT. Biosci Biotechnol Biochem. 2004 Apr;68(4):808-13.

2003

Nakashima H, Fukuchi S, Nishikawa K.
Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo). 2003 Apr;133(4):507-13.

Kashiwagi K, Shiba K, Fukami-Kobayashi K, Noda T, Nishikawa K, Noguchi H.
Characterization of folding pathways of the type-1 and type-2 periplasmic binding proteins MglB and ArgT. J Biochem (Tokyo). 2003 Mar;133(3):371-6.

Ota M, Kinoshita K, Nishikawa K.
Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol. 2003 Apr 11;327(5):1053-64.

Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K.
Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol. 2003 Mar 21;327(2):347-57.

Fukami-Kobayashi K, Tateno Y, Nishikawa K.
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol. 2003 Feb;20(2):267-77.

2002

Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K.
GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 2002 Jan 1;30(1):294-8.

Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K.
A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene. 2002 Jul 10;294(1-2):25-33.

Isogai Y, Ota M, Ishii A, Ishida M, Nishikawa K.
Identification of amino acids involved in protein structural uniqueness: implication for de novo protein design. Protein Eng. 2002 Jul;15(7):555-60.

Nishikawa K.
Information concept in biology. Bioinformatics. 2002 May;18(5):649-51.

2001

Kinjo AR, Nishikawa K.
Comparison of energy components of proteins from thermophilic and mesophilic organisms. Eur Biophys J. 2001 Sep;30(5):378-84.

Ota M, Isogai Y, Nishikawa K.
Knowledge-based potential defined for a rotamer library to design protein sequences. Protein Eng. 2001 Aug;14(8):557-64.

Fukuchi S, Nishikawa K.
Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J Mol Biol. 2001 Jun 15;309(4):835-43.

Kinjo AR, Kidera A, Nakamura H, Nishikawa K.
Physicochemical evaluation of protein folds predicted by threading. Eur Biophys J. 2001;30(1):1-10.

2000

Kawabata T, Arisaka F, Nishikawa K.
Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches. Gene. 2000 Dec 23;259(1-2):223-33.

Kawabata T, Nishikawa K.
Protein structure comparison using the markov transition model of evolution. Proteins. 2000 Oct 1;41(1):108-22.

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. 2000 May 16;39(19):5683-90.

1999

Ota M, Kawabata T, Kinjo AR, Nishikawa K.
Cooperative approach for the protein fold recognition. Proteins. 1999;Suppl 3:126-32.

Nagano N, Ota M, Nishikawa K.
Strong hydrophobic nature of cysteine residues in proteins. FEBS Lett. 1999 Sep 10;458(1):69-71.

Takano K, Ota M, Ogasahara K, Yamagata Y, Nishikawa K, Yutani K.
Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Protein Eng. 1999 Aug;12(8):663-72.

Isogai Y, Ota M, Fujisawa T, Izuno H, Mukai M, Nakamura H, Iizuka T, Nishikawa K.
Design and synthesis of a globin fold. Biochemistry. 1999 Jun 8;38(23):7431-43.

Ota M, Nishikawa K.
Feasibility in the inverse protein folding protocol. Protein Sci. 1999 May;8(5):1001-9.

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. 1999 Feb 12;286(1):279-90.

Kawabata T, Ota M, Nishikawa K.
The Protein Mutant Database. Nucleic Acids Res. 1999 Jan 1;27(1):355-7.

■■■ Laboratory for Gene-Product Informatics ■■■