Nakamura S - Search Results

1

Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

Tsujikawa H, Sato K, Wei C, Saad G, Sumikoshi K, Nakamura S, Terada T, Shimizu K. Tsujikawa H, et al. Among authors: nakamura s. J Struct Funct Genomics. 2016 Sep;17(2-3):39-49. doi: 10.1007/s10969-016-9204-2. Epub 2016 Jul 11. J Struct Funct Genomics. 2016. PMID: 27400687 Free PMC article.

2

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.

Morita M, Nakamura S, Shimizu K. Morita M, et al. Among authors: nakamura s. Proteins. 2008 Nov 1;73(2):468-79. doi: 10.1002/prot.22067. Proteins. 2008. PMID: 18452211

3

Development of a sugar-binding residue prediction system from protein sequences using support vector machine.

Banno M, Komiyama Y, Cao W, Oku Y, Ueki K, Sumikoshi K, Nakamura S, Terada T, Shimizu K. Banno M, et al. Among authors: nakamura s. Comput Biol Chem. 2017 Feb;66:36-43. doi: 10.1016/j.compbiolchem.2016.10.009. Epub 2016 Nov 9. Comput Biol Chem. 2017. PMID: 27889654 Free article.

4

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: nakamura s. Genome Inform. 2003;14:228-37. Genome Inform. 2003. PMID: 15706537

5

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: nakamura s. 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.

6

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: nakamura s. 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.

7

Potential for assessing quality of protein structure based on contact number prediction.

Ishida T, Nakamura S, Shimizu K. Ishida T, et al. Among authors: nakamura s. Proteins. 2006 Sep 1;64(4):940-7. doi: 10.1002/prot.21047. Proteins. 2006. PMID: 16788993

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: nakamura s. 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: nakamura s. 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

Using a new GPI-anchored-protein identification system to mine the protein databases of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae.

Cao W, Maruyama J, Kitamoto K, Sumikoshi K, Terada T, Nakamura S, Shimizu K. Cao W, et al. Among authors: nakamura s. J Gen Appl Microbiol. 2009 Oct;55(5):381-93. doi: 10.2323/jgam.55.381. J Gen Appl Microbiol. 2009. PMID: 19940384 Free article.

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