Taiji M - Search Results

1

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach.

Narumi T, Yasuoka K, Taiji M, Höfinger S. Narumi T, et al. Among authors: taiji m. J Comput Chem. 2009 Nov 15;30(14):2351-7. doi: 10.1002/jcc.21257. J Comput Chem. 2009. PMID: 19350574

2

Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.

Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, Ebisuzaki T, Hoek JB, Konagaya A, Kholodenko BN. Suenaga A, et al. Among authors: taiji m. J Biol Chem. 2004 Feb 6;279(6):4657-62. doi: 10.1074/jbc.M310598200. Epub 2003 Nov 12. J Biol Chem. 2004. PMID: 14613932 Free article.

3

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations.

Okimoto N, Futatsugi N, Fuji H, Suenaga A, Morimoto G, Yanai R, Ohno Y, Narumi T, Taiji M. Okimoto N, et al. Among authors: taiji m. PLoS Comput Biol. 2009 Oct;5(10):e1000528. doi: 10.1371/journal.pcbi.1000528. Epub 2009 Oct 9. PLoS Comput Biol. 2009. PMID: 19816553 Free PMC article.

4

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.

Suenaga A, Takada N, Hatakeyama M, Ichikawa M, Yu X, Tomii K, Okimoto N, Futatsugi N, Narumi T, Shirouzu M, Yokoyama S, Konagaya A, Taiji M. Suenaga A, et al. Among authors: taiji m. J Biol Chem. 2005 Jan 14;280(2):1321-6. doi: 10.1074/jbc.M410436200. Epub 2004 Nov 1. J Biol Chem. 2005. PMID: 15520002 Free article.

5

Folding dynamics of 10-residue beta-hairpin peptide chignolin.

Suenaga A, Narumi T, Futatsugi N, Yanai R, Ohno Y, Okimoto N, Taiji M. Suenaga A, et al. Among authors: taiji m. Chem Asian J. 2007 May 4;2(5):591-8. doi: 10.1002/asia.200600385. Chem Asian J. 2007. PMID: 17465405

6

Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides.

Suenaga A, Hatakeyama M, Ichikawa M, Yu X, Futatsugi N, Narumi T, Fukui K, Terada T, Taiji M, Shirouzu M, Yokoyama S, Konagaya A. Suenaga A, et al. Among authors: taiji m. Biochemistry. 2003 May 13;42(18):5195-200. doi: 10.1021/bi034113h. Biochemistry. 2003. PMID: 12731860

7

Structure and dynamics of RNA polymerase II elongation complex.

Suenaga A, Okimoto N, Futatsugi N, Hirano Y, Narumi T, Ohno Y, Yanai R, Hirokawa T, Ebisuzaki T, Konagaya A, Taiji M. Suenaga A, et al. Among authors: taiji m. Biochem Biophys Res Commun. 2006 Apr 28;343(1):90-8. doi: 10.1016/j.bbrc.2006.02.124. Epub 2006 Mar 2. Biochem Biophys Res Commun. 2006. PMID: 16529717

8

A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

Yamagishi J, Okimoto N, Morimoto G, Taiji M. Yamagishi J, et al. Among authors: taiji m. J Comput Chem. 2014 Nov 5;35(29):2132-9. doi: 10.1002/jcc.23728. Epub 2014 Sep 15. J Comput Chem. 2014. PMID: 25220475 Free PMC article.

9

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.

Kikugawa G, Apostolov R, Kamiya N, Taiji M, Himeno R, Nakamura H, Yonezawa Y. Kikugawa G, et al. Among authors: taiji m. J Comput Chem. 2009 Jan 15;30(1):110-8. doi: 10.1002/jcc.21035. J Comput Chem. 2009. PMID: 18524021

10

Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.

Otsuka T, Okimoto N, Taiji M. Otsuka T, et al. Among authors: taiji m. J Comput Chem. 2015 Nov 15;36(30):2209-18. doi: 10.1002/jcc.24055. Epub 2015 Sep 24. J Comput Chem. 2015. PMID: 26400829

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