Harada R - Search Results

1

Reduced native state stability in crowded cellular environment due to protein-protein interactions.

Harada R, Tochio N, Kigawa T, Sugita Y, Feig M. Harada R, et al. J Am Chem Soc. 2013 Mar 6;135(9):3696-701. doi: 10.1021/ja3126992. Epub 2013 Feb 20. J Am Chem Soc. 2013. PMID: 23402619 Free PMC article.

2

Protein crowding affects hydration structure and dynamics.

Harada R, Sugita Y, Feig M. Harada R, et al. J Am Chem Soc. 2012 Mar 14;134(10):4842-9. doi: 10.1021/ja211115q. Epub 2012 Mar 2. J Am Chem Soc. 2012. PMID: 22352398 Free PMC article.

3

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins.

Harada R, Takano Y, Shigeta Y. Harada R, et al. J Chem Phys. 2014 Mar 28;140(12):125103. doi: 10.1063/1.4869594. J Chem Phys. 2014. PMID: 24697482

4

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

Feig M, Harada R, Mori T, Yu I, Takahashi K, Sugita Y. Feig M, et al. Among authors: harada r. J Mol Graph Model. 2015 May;58:1-9. doi: 10.1016/j.jmgm.2015.02.004. Epub 2015 Feb 28. J Mol Graph Model. 2015. PMID: 25765281 Free PMC article.

5

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Yu I, et al. Among authors: harada r. Elife. 2016 Nov 1;5:e19274. doi: 10.7554/eLife.19274. Elife. 2016. PMID: 27801646 Free PMC article.

6

Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins.

Harada R, Shigeta Y. Harada R, et al. J Chem Theory Comput. 2017 Mar 14;13(3):1411-1423. doi: 10.1021/acs.jctc.6b01112. Epub 2017 Feb 22. J Chem Theory Comput. 2017. PMID: 28170260

7

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway.

Harada R, Kitao A. Harada R, et al. J Chem Phys. 2013 Jul 21;139(3):035103. doi: 10.1063/1.4813023. J Chem Phys. 2013. PMID: 23883057

8

Simple, yet powerful methodologies for conformational sampling of proteins.

Harada R, Takano Y, Baba T, Shigeta Y. Harada R, et al. Phys Chem Chem Phys. 2015 Mar 7;17(9):6155-73. doi: 10.1039/c4cp05262e. Phys Chem Chem Phys. 2015. PMID: 25659594

9

Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins.

Harada R, Kitao A. Harada R, et al. J Chem Theory Comput. 2015 Nov 10;11(11):5493-502. doi: 10.1021/acs.jctc.5b00723. Epub 2015 Oct 21. J Chem Theory Comput. 2015. PMID: 26574337

10

Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches.

Harada R, Shigeta Y. Harada R, et al. J Chem Inf Model. 2017 Dec 26;57(12):3070-3078. doi: 10.1021/acs.jcim.7b00573. Epub 2017 Nov 16. J Chem Inf Model. 2017. PMID: 29111731

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