Matsunaga Y - Search Results

1

Explicit description of viral capsid subunit shapes by unfolding dihedrons.

Toyooka R, Nishimoto S, Tendo T, Horiyama T, Tachi T, Matsunaga Y. Toyooka R, et al. Among authors: matsunaga y. Commun Biol. 2024 Nov 14;7(1):1509. doi: 10.1038/s42003-024-07218-x. Commun Biol. 2024. PMID: 39543373 Free PMC article.

2

Influence of structural symmetry on protein dynamics.

Matsunaga Y, Koike R, Ota M, Tame JR, Kidera A. Matsunaga Y, et al. PLoS One. 2012;7(11):e50011. doi: 10.1371/journal.pone.0050011. Epub 2012 Nov 26. PLoS One. 2012. PMID: 23189176 Free PMC article.

3

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.

Niina T, Matsunaga Y, Takada S. Niina T, et al. Among authors: matsunaga y. PLoS Comput Biol. 2021 Jul 20;17(7):e1009215. doi: 10.1371/journal.pcbi.1009215. eCollection 2021 Jul. PLoS Comput Biol. 2021. PMID: 34283829 Free PMC article.

4

Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.

Fujisaki H, Moritsugu K, Matsunaga Y. Fujisaki H, et al. Among authors: matsunaga y. Int J Mol Sci. 2018 Oct 15;19(10):3177. doi: 10.3390/ijms19103177. Int J Mol Sci. 2018. PMID: 30326661 Free PMC article.

5

Minimum free energy path of ligand-induced transition in adenylate kinase.

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A. Matsunaga Y, et al. PLoS Comput Biol. 2012;8(6):e1002555. doi: 10.1371/journal.pcbi.1002555. Epub 2012 Jun 7. PLoS Comput Biol. 2012. PMID: 22685395 Free PMC article.

6

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

Kobayashi C, Matsunaga Y, Koike R, Ota M, Sugita Y. Kobayashi C, et al. Among authors: matsunaga y. J Phys Chem B. 2015 Nov 19;119(46):14584-93. doi: 10.1021/acs.jpcb.5b07668. Epub 2015 Nov 4. J Phys Chem B. 2015. PMID: 26536148

7

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins.

Shinobu A, Kobayashi C, Matsunaga Y, Sugita Y. Shinobu A, et al. Among authors: matsunaga y. J Chem Inf Model. 2021 May 24;61(5):2427-2443. doi: 10.1021/acs.jcim.1c00286. Epub 2021 May 6. J Chem Inf Model. 2021. PMID: 33956432

8

End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images.

Matsunaga Y, Fuchigami S, Ogane T, Takada S. Matsunaga Y, et al. Sci Rep. 2023 Jan 4;13(1):129. doi: 10.1038/s41598-022-27057-2. Sci Rep. 2023. PMID: 36599879 Free PMC article.

9

How many dimensions are required to approximate the potential energy landscape of a model protein?

Komatsuzaki T, Hoshino K, Matsunaga Y, Rylance GJ, Johnston RL, Wales DJ. Komatsuzaki T, et al. Among authors: matsunaga y. J Chem Phys. 2005 Feb 22;122(8):84714. doi: 10.1063/1.1854123. J Chem Phys. 2005. PMID: 15836084

10

Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior.

Ishizone T, Matsunaga Y, Fuchigami S, Nakamura K. Ishizone T, et al. Among authors: matsunaga y. J Chem Theory Comput. 2024 Jan 9;20(1):436-450. doi: 10.1021/acs.jctc.3c01025. Epub 2023 Dec 27. J Chem Theory Comput. 2024. PMID: 38151233

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