Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 20 of 21

1.
2.

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

Matsunaga Y, Sugita Y.

Elife. 2018 May 3;7. pii: e32668. doi: 10.7554/eLife.32668.

3.

Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB.

Matsunaga Y, Yamane T, Terada T, Moritsugu K, Fujisaki H, Murakami S, Ikeguchi M, Kidera A.

Elife. 2018 Mar 6;7. pii: e31715. doi: 10.7554/eLife.31715.

4.

Tumor invasion to the arteries feeding the gallbladder as a novel risk factor for cholecystitis after metallic stent placement in distal malignant biliary obstruction.

Sogabe Y, Kodama Y, Honjo H, Aoyama I, Muramoto Y, Koga E, Yanaidani T, Kawai M, Yoshikawa T, Matsumoto S, Matsumoto A, Mori Y, Ono C, Nishida M, Nishida Y, Mikami T, Matsunaga Y, Miyamoto Y, Kitami M, Nishikawa K, Kondo M, Miyake N, Kawanami C, Seno H.

Dig Endosc. 2018 May;30(3):380-387. doi: 10.1111/den.12991. Epub 2017 Dec 21.

PMID:
29181859
5.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

Kobayashi C, Jung J, Matsunaga Y, Mori T, Ando T, Tamura K, Kamiya M, Sugita Y.

J Comput Chem. 2017 Sep 30;38(25):2193-2206. doi: 10.1002/jcc.24874. Epub 2017 Jul 18.

PMID:
28718930
6.

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein.

Matsunaga Y, Komuro Y, Kobayashi C, Jung J, Mori T, Sugita Y.

J Phys Chem Lett. 2016 Apr 21;7(8):1446-51. doi: 10.1021/acs.jpclett.6b00317. Epub 2016 Apr 6.

PMID:
27049936
7.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

Jung J, Mori T, Kobayashi C, Matsunaga Y, Yoda T, Feig M, Sugita Y.

Wiley Interdiscip Rev Comput Mol Sci. 2015 Jul;5(4):310-323. Epub 2015 May 7.

8.

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

Kobayashi C, Matsunaga Y, Koike R, Ota M, Sugita Y.

J Phys Chem B. 2015 Nov 19;119(46):14584-93. doi: 10.1021/acs.jpcb.5b07668. Epub 2015 Nov 4.

PMID:
26536148
9.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L.

Front Bioeng Biotechnol. 2015 Sep 3;3:125. doi: 10.3389/fbioe.2015.00125. eCollection 2015. Review.

10.

Sequential data assimilation for single-molecule FRET photon-counting data.

Matsunaga Y, Kidera A, Sugita Y.

J Chem Phys. 2015 Jun 7;142(21):214115. doi: 10.1063/1.4921983.

PMID:
26049487
11.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

Matsunaga Y, Baba A, Li CB, Straub JE, Toda M, Komatsuzaki T, Berry RS.

J Chem Phys. 2013 Dec 7;139(21):215101. doi: 10.1063/1.4834415.

PMID:
24320403
12.

Influence of structural symmetry on protein dynamics.

Matsunaga Y, Koike R, Ota M, Tame JR, Kidera A.

PLoS One. 2012;7(11):e50011. doi: 10.1371/journal.pone.0050011. Epub 2012 Nov 26.

13.

[A case of endocrine carcinoma of the cecum treated with CDDP/VP-16].

Hiramoto S, Mizota A, Yoshioka A, Zaima C, Sogabe Y, Hieda N, Nishida Y, Mizuguchi A, Kakiuchi N, Matsunaga Y, Yasumura S, Kuriyama K, Hidaka K, Tanabe W, Honjo H, Hasegawa K, Kondo M, Nishikawa K, Miyake N, Kawanami C, Shirase T.

Gan To Kagaku Ryoho. 2012 Aug;39(8):1255-8. Japanese.

PMID:
22902453
14.

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

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A.

PLoS Comput Biol. 2012;8(6):e1002555. doi: 10.1371/journal.pcbi.1002555. Epub 2012 Jun 7.

15.

Cooperativity at different space and time scales in multiscale protein dynamics.

Matsunaga Y, Li CB, Komatsuzaki T.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 2):016213. Epub 2010 Jul 19.

PMID:
20866713
16.

Multivariate frequency domain analysis of protein dynamics.

Matsunaga Y, Fuchigami S, Kidera A.

J Chem Phys. 2009 Mar 28;130(12):124104. doi: 10.1063/1.3090812.

PMID:
19334805
17.

Schwannoma of the brachial plexus presenting as an enlarging cystic mass: report of a case.

Chen F, Miyahara R, Matsunaga Y, Koyama T.

Ann Thorac Cardiovasc Surg. 2008 Oct;14(5):311-3.

PMID:
18989247
18.

Anomalous diffusion in folding dynamics of minimalist protein landscape.

Matsunaga Y, Li CB, Komatsuzaki T.

Phys Rev Lett. 2007 Dec 7;99(23):238103. Epub 2007 Dec 6.

PMID:
18233416
19.

Topographical complexity of multidimensional energy landscapes.

Rylance GJ, Johnston RL, Matsunaga Y, Li CB, Baba A, Komatsuzaki T.

Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18551-5. Epub 2006 Nov 28.

20.

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

Li CB, Matsunaga Y, Toda M, Komatsuzaki T.

J Chem Phys. 2005 Nov 8;123(18):184301.

PMID:
16292902

Supplemental Content

Loading ...
Support Center