K. Nishikawa

发表

Comparison of protein structures using 3D profile alignment

M. Suyama, Y. Matsuo, K. Nishikawa, 2009, Journal of Molecular Evolution.

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

K. Nishikawa, M. Ota, K. Kinoshita, 2003, Journal of molecular biology.

Assessment of secondary-structure prediction of proteins. Comparison of computerized Chou-Fasman method with others.

K. Nishikawa, 1983, Biochimica et biophysica acta.

Protein structure comparison using the Markov transition model of evolution

K. Nishikawa, T. Kawabata, 2000, Proteins.

Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria.

K. Nishikawa, S. Fukuchi, 2001, Journal of molecular biology.

Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies.

Y. Matsuo, K. Nishikawa, Y. Matsuo, 1993, Protein engineering.

Predicting absolute contact numbers of native protein structure from amino acid sequence

K. Nishikawa, A. Kinjo, K. Horimoto, 2004, Proteins.

Radial locations of amino acid residues in a globular protein: correlation with the sequence.

K. Nishikawa, T. Ooi, 1986, Journal of biochemistry.

Prediction of the structural similarity between spermidine/putrescine‐binding protein and maltose‐binding protein

Y. Matsuo, K. Nishikawa, 1994, FEBS letters.

Cooperative approach for the protein fold recognition

K. Nishikawa, M. Ota, T. Kawabata, 1999, Proteins.

Protein structural similarities predicted by a sequence‐structure compatibility method

Y. Matsuo, K. Nishikawa, 1994, Protein science : a publication of the Protein Society.

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, H. Mewes, 2004, PLoS Biology.

Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

Takashi Gojobori, Satoshi Fukuchi, K. Nishikawa, 2009, BMC Structural Biology.

A tree of life based on protein domain organizations.

K. Nishikawa, Y. Tateno, K. Fukami-Kobayashi, 2007, Molecular biology and evolution.

Estimation of the number of authentic orphan genes in bacterial genomes.

K. Nishikawa, S. Fukuchi, 2004, DNA research : an international journal for rapid publication of reports on genes and genomes.

Unique amino acid composition of proteins in halophilic bacteria.

Satoshi Fukuchi, K. Nishikawa, S. Fukuchi, 2003, Journal of molecular biology.

Title Compositional changes in RNA , DNA and proteins for bacterial adaptationto higher and lower temperatures

K. Nishikawa, S. Fukuchi, H. Nakashima, 2014 .

The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins

K Nishikawa, K. Nishikawa, H. Nakashima, 1992, FEBS letters.

Structure of the F-spondin reeler domain reveals a unique beta-sandwich fold with a deformable disulfide-bonded loop.

Junichi Takagi, K. Nishikawa, J. Takagi, 2008, Acta crystallographica. Section D, Biological crystallography.

Constructing a protein mutant database.

K. Nishikawa, S. Ishino, H. Takenaka, 1994, Protein engineering.

Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution.

K. Nishikawa, Y. Kubota, T. Ooi, 1983, Journal of biochemistry.

Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types.

K. Nishikawa, Y. Kubota, T. Ooi, 1983, Journal of biochemistry.

Mutation in aspartic acid residues modifies catalytic and haemolytic activities of Bacillus cereus sphingomyelinase.

Y. Matsuo, K. Nishikawa, M. Tomita, 1995, The Biochemical journal.

Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history.

K. Nishikawa, Y. Tateno, K. Fukami-Kobayashi, 1999, Journal of molecular biology.

Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation.

K. Nishikawa, A. Kinjo, Keiichi Homma, 2006, Journal of molecular biology.

Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.

Satoshi Fukuchi, Hiroshi Nakashima, K. Nishikawa, 2003, Journal of biochemistry.

Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies.

K Nishikawa, K. Nishikawa, H. Nakashima, 1994, Journal of molecular biology.

Genes from nine genomes are separated into their organisms in the dinucleotide composition space.

K Nishikawa, K. Nishikawa, T. Ooi, 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

Discrimination of intracellular and extracellular proteins by single residue and residue-pair scores

K. Nishikawa, H. Nakashima, 1994 .

Computational Prediction of O-linked Glycosylation Sites That Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins

Ikuko Nishikawa, Satoshi Fukuchi, Masahiro Ito, 2010, International journal of molecular sciences.

Correlation of the amino acid composition of a protein to its structural and biological characters.

K Nishikawa, K. Nishikawa, T. Ooi, 1982, Journal of biochemistry.

The folding type of a protein is relevant to the amino acid composition.

K Nishikawa, K. Nishikawa, T. Ooi, 1986, Journal of biochemistry.

Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence

Akira R. Kinjo, K. Nishikawa, A. Kinjo, 2005 .

Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks

Akira R. Kinjo, K. Nishikawa, A. Kinjo, 2005, Biophysics.

Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods.

K Nishikawa, K. Nishikawa, T. Ooi, 1986, Biochimica et biophysica acta.

Predicting protein secondary structure based on amino acid sequence.

K Nishikawa, K. Nishikawa, T. Noguchi, 1991, Methods in enzymology.

Prediction of the surface-interior diagram of globular proteins by an empirical method.

K Nishikawa, K. Nishikawa, T. Ooi, 2009, International journal of peptide and protein research.

Assessment of a protein fold recognition method that takes into account four physicochemical properties: Side‐chain packing, solvation, hydrogen‐bonding, and local conformation

K Nishikawa, Y. Matsuo, K. Nishikawa, 1995, Proteins.

Correction: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, Gopal R. Gopinath, 2004, PLoS biology.

Identification of amino acids involved in protein structural uniqueness: implication for de novo protein design.

K. Nishikawa, M. Ota, Y. Isogai, 2002, Protein engineering.

Binary classification of protein molecules into intrinsically disordered and ordered segments

Takashi Gojobori, Satoshi Fukuchi, Kazuo Hosoda, 2011, BMC Structural Biology.

Intrinsically disordered regions of human plasma membrane proteins preferentially occur in the cytoplasmic segment.

K. Nishikawa, Keiichi Homma, Y. Minezaki, 2007, Journal of molecular biology.

Segmentation of a protein into structural elements: Analysis and classification of segments

K Nishikawa, K. Nishikawa, T. Ooi, 1988, Journal of protein chemistry.

Ja n 20 05 Recoverable One-dimensional Encoding of Protein Three-dimensional Structures

K. Nishikawa, A. Kinjo, 2005 .

Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea.

K. Nishikawa, Keiichi Homma, Y. Minezaki, 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.

K. Nishikawa, Y. Tateno, K. Fukami-Kobayashi, 2003, Molecular biology and evolution.

Threading Protein Sequences

K. Nishikawa, 2002 .

Alternative splice variants encoding unstable protein domains exist in the human brain.

K. Nishikawa, T. Nagase, O. Ohara, 2004, Journal of molecular biology.

A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.

K. Nishikawa, M. Ota, T. Kawabata, 2002, Gene.

A Web Site for Location to Location Correspondence (L2LC): Circular Genome Comparison from Related Gene Configuration

K. Nishikawa, S. Fukuchi, K. Horimoto, 2002 .

Sequencing and characterization of the kinesin-related geneskatB andkatC ofArabidopsis thaliana

K. Nishikawa, K. Shinozaki, K. Yamaguchi-Shinozaki, 1994, Plant Molecular Biology.

Structural and functional properties of designed globins

K. Nishikawa, M. Ota, T. Iizuka, 2000 .

Prediction of Protein-Destabilizing Polymorphisms by Manual Curation with Protein Structure

K. Nishikawa, Yoshiharu Sato, S. Minoshima, 2012, PloS one.

Homology between mammalian DNA polymerase beta and terminal deoxynucleotidyltransferase.

K. Nishikawa, T. Ooi, M. Yamaguchi, 1987, The Journal of biological chemistry.

Redesign of Artificial Globins: Effects of Residue Replacements at Hydrophobic Sites on the Structural Properties†

K. Nishikawa, M. Ota, T. Fujisawa, 2000 .

Tertiary structural models for human interleukin‐6 and evaluation by a sequence‐structure compatibility method and NMR experimental information

Y. Matsuo, K. Nishikawa, E. Suzuki, 1997, FEBS letters.

Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.

K. Nishikawa, M. Ota, T. Fujisawa, 2000, Biochemistry.

Solvent Effects on a Protein Molecule : A Theoretical Inspection

K. Nishikawa, 1983 .

A Genome Tree Made from Information on Protein Domain Organizations

K. Nishikawa, K. Fukami-Kobayashi, 2008 .

Exclusive expression of C. elegans osm-3 kinesin gene in chemosensory neurons open to the external environment.

K. Nishikawa, Z. Siddiqui, M. Tabish, 1995, Journal of Molecular Biology.

Trifluoroethanol-induced Stabilization of the α-Helical Structure of β-Lactoglobulin: Implication for Non-hierarchical Protein Folding

K. Nishikawa, K. Shiraki, Y. Goto, 1995 .

Analysis of Amino Acid Residues Involved in Catalysis of Polyethylene Glycol Dehydrogenase from Sphingopyxis terrae, Using Three-Dimensional Molecular Modeling-Based Kinetic Characterization of Mutants

K. Nishikawa, T. Kawabata, A. Tani, 2006, Applied and Environmental Microbiology.

Mutants Modeling-Based Kinetic Characterization of Using Three-Dimensional Molecular , Sphingopyxis terrae Dehydrogenase from in Catalysis of Polyethylene Glycol Analysis of Amino Acid Residues Involved

K. Nishikawa, T. Kawabata, A. Tani, 2006 .

Trifluoroethanol-induced stabilization of the alpha-helical structure of beta-lactoglobulin: implication for non-hierarchical protein folding.

K. Nishikawa, K. Shiraki, Y. Goto, 1995, Journal of molecular biology.

Molecular cloning of a cDNA of a camptothecin-resistant human DNA topoisomerase I and identification of mutation sites

Eric Patterson, Ken Nishikawa, Ryutaro Yamada, 1991, Nucleic Acids Res..

Characterization of vitelline membrane outer layer protein I, VMO-I: amino acid sequence and structural stability.

K. Nishikawa, E. Morishita, H. Narita, 1995, Journal of Biochemistry (Tokyo).

Natively unfolded proteins: An overview

K. Nishikawa, 2009, Biophysics.

An Overview on Natively Unfolded Proteins

K. Nishikawa, 2009 .

GTOP: a database of protein structures predicted from genome sequences

Takeshi Kawabata, Motonori Ota, Keiichi Homma, 2002, Nucleic Acids Res..

Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.

K Nishikawa, K. Nishikawa, T. Kawabata, 2000, Gene.

Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution

Akira R. Kinjo, K. Nishikawa, A. Kinjo, 2014, Biophysics.

Essential role of long non-coding RNAs in de novo chromatin modifications: the genomic address code hypothesis

K. Nishikawa, A. Kinjo, 2017, Biophysical Reviews.

forming the ligand-binding site ion-channel receptors shows SH 2-like and SH 3-like domains Predicted structure of the extracellular region of ligand-gated

K. Nishikawa, P. Schofield, S. Ranganathan, 2002 .

Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation

K. Nishikawa, T. Gojobori, S. Fukuchi, 2006, q-bio/0609018.

A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies.

K. Nishikawa, H. Mori, H. Sugawara, 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

What’s in a name? Why these proteins are intrinsically disordered

Sonia Longhi, Burkhard Rost, Zoran Obradovic, 2013, Intrinsically disordered proteins.

Physicochemical evaluation of protein folds predicted by threading

K. Nishikawa, Haruki Nakamura, A. Kidera, 2000, European Biophysics Journal.

The Protein Mutant Database

Motonori Ota, Ken Nishikawa, Takeshi Kawabata, 1999, Nucleic Acids Res..

Intrinsically disordered loops inserted into the structural domains of human proteins.

Satoshi Fukuchi, K. Nishikawa, S. Fukuchi, 2006, Journal of molecular biology.

Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-Proteobacteria.

Takashi Gojobori, Satoshi Fukuchi, Yoji Nakamura, 2007, Molecular biology and evolution.

Mechanism of evolution by genetic assimilation

K. Nishikawa, A. Kinjo, 2018, Biophysical Reviews.

Mechanism of evolution by genetic assimilation: Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression

K. Nishikawa, A. Kinjo, 2018, bioRxiv.

Tertiary Structure of Proteins. I. : Representation and Computation of the Conformations

Nobuhiko Saitô, Tatsuo Ooi, K. Nishikawa, 1972 .

Differences in dinucleotide frequencies of human, yeast, and Escherichia coli genes.

K Nishikawa, K. Nishikawa, T. Ooi, 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, 2008, Nucleic Acids Res..

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Teruyoshi Hishiki, Katsuhiko Murakami, Yoshihiro Kawahara, 2007, Nucleic Acids Res..

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

Y. Matsuo, K. Nishikawa, H. Ikezawa, 1996, Protein science : a publication of the Protein Society.

Strong hydrophobic nature of cysteine residues in proteins

K Nishikawa, K. Nishikawa, M. Ota, 1999, FEBS letters.

Cooperation between genetic mutations and phenotypic plasticity can bypass the Weismann barrier: The cooperative model of evolution

K. Nishikawa, A. Kinjo, 2013, 1309.4952.

Comparison of amino acid sequences between phosphoenolpyruvate carboxylases from Escherichia coli (allosteric) and Anacystis nidulans (non-allosteric): identification of conserved and variable regions.

K. Nishikawa, T. Ooi, F. Katagiri, 1985, Biochemical and biophysical research communications.

Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd.

K. Nishikawa, R. Kikuno, M. Khan, 1997, Journal of molecular biology.

Correspondence of homologies in amino acid sequence and tertiary structure of protein molecules.

K Nishikawa, K. Nishikawa, Y. Kubota, 1982, Biochimica et biophysica acta.

Conformational Properties of Poly(L-proline) Containing a Flexible Pyrrolidine Ring

K. Nishikawa, T. Ooi, W. Mattice, 1973 .

Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins

Akira R. Kinjo, Ken Nishikawa, K. Nishikawa, 2004, Bioinform..

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

K. Nishikawa, M. Ota, S. Kanaya, 2006, Journal of biotechnology.

Comparison of homologous tertiary structures of proteins.

K Nishikawa, K. Nishikawa, T. Ooi, 1974, Journal of theoretical biology.

A geometrical constraint approach for reproducing the native backbone conformation of a protein

K Nishikawa, K. Nishikawa, T Nakai, 1993, Proteins.

Identification of a gene family (kat) encoding kinesin-like proteins in Arabidopsis thaliana and the characterization of secondary structure of KatA

K. Nishikawa, K. Yamaguchi-Shinozaki, K. Shinozaki, 1993, Molecular and General Genetics MGG.

Structural model of the ATP‐binding domain of the F1‐β subunit based on analogy to the RecA protein

Y. Matsuo, K. Nishikawa, Masasuke Yoshida, 1994, FEBS letters.

Knowledge-based potential defined for a rotamer library to design protein sequences.

K Nishikawa, K. Nishikawa, M. Ota, 2001, Protein engineering.

Design and synthesis of a globin fold.

K Nishikawa, K. Nishikawa, M. Ota, 1999, Biochemistry.

Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins.

K Nishikawa, K. Nishikawa, M. Ota, 1997, Protein engineering.

Ja n 20 05 Recoverable One-dimensional Encoding of Protein Three-dimensional Structures

K. Nishikawa, A. Kinjo, 2005 .

Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions.

K Nishikawa, Y. Matsuo, K. Nishikawa, 1995, Journal of biochemistry.

Prediction of protein secondary structure using the 3D-1D compatibility algorithm

Masahiro Ito, Yo Matsuo, Ken Nishikawa, 1997, Comput. Appl. Biosci..

Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins

K Nishikawa, K. Nishikawa, T. Ooi, 1990, Proteins.

C. elegans KLP-11/OSM-3/KAP-1: orthologs of the sea urchin kinesin-II, and mouse KIF3A/KIFB/KAP3 kinesin complexes.

K. Nishikawa, M. Khan, M. Y. Ali, 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

Intrinsically disordered regions have specific functions in mitochondrial and nuclear proteins.

K. Nishikawa, H. Sugawara, S. Fukuchi, 2012, Molecular bioSystems.

Structural requirement of highly‐conserved residues in globins

K Nishikawa, K. Nishikawa, M. Ota, 1997, FEBS letters.

Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.

K Nishikawa, K. Nishikawa, M. Ota, 1999, Protein engineering.

Prediction of protein phosphorylation sites by support vector machines

Yukako Tohsato, Ikuko Nishikawa, Ken Nishikawa, 2013, 2013 6th International Conference on Biomedical Engineering and Informatics.

Intrinsically disordered proteins in human mitochondria

K. Nishikawa, S. Fukuchi, I. Nishikawa, 2012, Genes to cells : devoted to molecular & cellular mechanisms.

The folding type of a protein is relevant to the amino acid composition.

K. Nishikawa, T. Ooi, H. Nakashima, 1986, Journal of biochemistry.

Protein thermostabilization requires a fine-tuned placement of surface-charged residues.

K. Nishikawa, S. Fukuchi, S. Kanaya, 2007, Journal of biochemistry.

Mechanism of evolution by genetic assimilation

K. Nishikawa, A. Kinjo, 2018, Biophysical Reviews.

Detection of weak sequence homology of proteins for tertiary structure prediction.

K. Nishikawa, T. Ooi, H. Nakashima, 1987, Protein sequences & data analysis.