Shimizu K - Search Results

1

Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.

Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S. Miyake M, et al. Among authors: shimizu k. FEBS J. 2020 Dec;287(23):5114-5129. doi: 10.1111/febs.15315. Epub 2020 Apr 17. FEBS J. 2020. PMID: 32246585 Free article.

2

Development of an ab initio protein structure prediction system ABLE.

Ishida T, Nishimura T, Nozaki M, Inoue T, Terada T, Nakamura S, Shimizu K. Ishida T, et al. Among authors: shimizu k. Genome Inform. 2003;14:228-37. Genome Inform. 2003. PMID: 15706537

3

Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01.

Dong X, Fushinobu S, Fukuda E, Terada T, Nakamura S, Shimizu K, Nojiri H, Omori T, Shoun H, Wakagi T. Dong X, et al. Among authors: shimizu k. J Bacteriol. 2005 Apr;187(7):2483-90. doi: 10.1128/JB.187.7.2483-2490.2005. J Bacteriol. 2005. PMID: 15774891 Free PMC article.

4

Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase.

Nojiri H, Ashikawa Y, Noguchi H, Nam JW, Urata M, Fujimoto Z, Uchimura H, Terada T, Nakamura S, Shimizu K, Yoshida T, Habe H, Omori T. Nojiri H, et al. Among authors: shimizu k. J Mol Biol. 2005 Aug 12;351(2):355-70. doi: 10.1016/j.jmb.2005.05.059. J Mol Biol. 2005. PMID: 16005887

5

Folding free-energy landscape of a 10-residue mini-protein, chignolin.

Satoh D, Shimizu K, Nakamura S, Terada T. Satoh D, et al. Among authors: shimizu k. FEBS Lett. 2006 Jun 12;580(14):3422-6. doi: 10.1016/j.febslet.2006.05.015. Epub 2006 May 11. FEBS Lett. 2006. PMID: 16709409 Free article.

6

ROKU: a novel method for identification of tissue-specific genes.

Kadota K, Ye J, Nakai Y, Terada T, Shimizu K. Kadota K, et al. Among authors: shimizu k. BMC Bioinformatics. 2006 Jun 12;7:294. doi: 10.1186/1471-2105-7-294. BMC Bioinformatics. 2006. PMID: 16764735 Free PMC article.

7

Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides.

Ishitani R, Shimizu K, Terada T. Ishitani R, et al. Among authors: shimizu k. J Chem Phys. 2006 Jun 7;124(21):214902. doi: 10.1063/1.2200698. J Chem Phys. 2006. PMID: 16774437

8

A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions.

Sumikoshi K, Terada T, Nakamura S, Shimizu K. Sumikoshi K, et al. Among authors: shimizu k. Genome Inform. 2005;16(2):161-73. Genome Inform. 2005. PMID: 16901099

9

Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop.

Yamasaki S, Nakamura S, Terada T, Shimizu K. Yamasaki S, et al. Among authors: shimizu k. Biophys J. 2007 Jan 1;92(1):192-200. doi: 10.1529/biophysj.106.093351. Epub 2006 Oct 6. Biophys J. 2007. PMID: 17028132 Free PMC article.

10

Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation.

Terada T, Satoh D, Mikawa T, Ito Y, Shimizu K. Terada T, et al. Among authors: shimizu k. Proteins. 2008 Nov 15;73(3):621-31. doi: 10.1002/prot.22100. Proteins. 2008. PMID: 18473359

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