論文 - 苙口　友隆

Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis

Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako

Journal of Synchrotron Radiation 23   312 - 323 2015年

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Classification of projection images of proteins with structural polymorphism by manifold; A simulation study for X-ray free-electron laser diffraction imaging

Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

Physical Review E 92 （ 3 ） 032710 2015年09月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Cryogenic coherent X-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA

Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi, Yu Masaki, Asahi Fukuda, Saki Hashimoto, Masayoshi Nakasako, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu, Yayoi Inui, Sachihiro Matsunaga, Takayuki Kato, Keiichi Namba, Keiichi Yamaguchi, Kazuo Kuwata, Hiroshi Kameda, Naoya Fukui, Yasushi Kawata, Takashi KameshimaYuki Takayama, Koji Yonekura, Masaki Yamamoto

Journal of Physics B: Atomic Molecular and Optical Physics 48 （ 18 ） 184003 2015年07月

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)

Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser

Yuki Takayama, Yayoi Inui Yuki Sekiguchi1, Amane Kobayashi, Tomotaka Oroguchi, Masaki Yamamoto, Sachihiro Matsunaga, Masayoshi Nakasako

Plant Cell Physiology 56 （ 7 ） 1272 - 1287 2015年07月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects

Yuki Takayama, Saori Maki-Yonekura, Tomotaka Oroguchi, Masayoshi Nakasako, Koji Yonekura

Scientific Reports 5   8074 2015年01月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging

Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, Masayoshi Nakasako

Optics Express 22 （ 23 ） 27892 - 27909 2014年11月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

IDATEN and G-SITENNO: GUI assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA

Yuki Sekiguchi, Masaki Yamamoto, Tomotaka Oroguchi, Yuki Takayama, Shigeyuki Suzuki, Masayoshi Nakasako

Journal of Synchrotron Radiation 21 （ 6 ） 1378 - 1383 2014年11月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Rui Xu, Huaidong Jiang, Changyong Song, Jose A. Rodriguez, Zhifeng Huang, Chien-Chun Chen, Daewoong Nam, Jaehyun Park, Marcus Gallagher-Jones, Sangsoo Kim, Sunam Kim, Akihiro Suzuki, Yuki Takayama, Tomotaka Oroguchi, Yukio Takahashi, Jiadong Fan, Yunfei Zou, Takaki Hatsui, Yuichi Inubushi, Takashi Kameshima, Koji Yonekura, Kensuke Tono, Tadashi Togashi,Takahiro Sato, Masaki Yamamoto, Masayoshi Nakasako, Makina Yabashi, Tetsuya Ishikawa, Jianwei Miao

Nature Communications 5   4061 2014年06月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Data processing software suite SITENNO for coherent X-ray diffraction imaging using X-ray free electron laser SACLA

Yuki Sekiguchi, Tomotaka Oroguchi, Yuki Takayama, Masayoshi Nakasako

Journal of Synchrotron Radiation 21 （ 3 ） 600 - 612 2014年03月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Light-induced conformational changes of LOV (Light Oxygen Voltage-sensing domain) 1 and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin

Koji Okajima, Yusuke Aihara, Yuki Takayama, Mihoko Nakajima, Sachiko Kashojiya, Takaaki Hikima, Tomotaka OroguchiAmane Kobayashi, Yuki Sekiguchi, Masaki Yamamoto, Tomomi Suzuki, Akira Nagatani, Masayoshi Nakasako, Satoru Tokutomi

Journal of Biological Chemistry 289 （ 1 ） 413 - 422 2014年01月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Coherent Diffraction Imaging Analysis of Shape-Controlled Nanoparticles with Focused Hard X-ray Free-Electron Laser Pulses

Yukio Takahashi, Akihiro Suzuki, Nobuyuki Zettsu, Tomotaka Oroguchi, Yuki Takayama, Yuki Sekiguchi, Amane Kobayashi, Masaki Yamamoto, Masayoshi Nakasako

Nano Letters 13 （ 12 ） 6028 - 6032 2013年12月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

Masayoshi Nakasako, Yuki Takayama, Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi, Keiya Shirahama, Masaki Yamamoto, Takaaki Hikima, Koji Yonekura, Saori Maki-Yonekura, Yoshiki Kohmura, Yuichi Inubushi, Yukio Takahashi , Akihiro Suzuki, Sachihiro Matsunaga, Yayoi Inui, Kensuke Tono, Takashi Kameshima, Yasumasa Joti, Takahiko Hoshi

Review of Scientific Instruments 84 （ 9 ） 093705 2013年09月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free electron laser diffraction imaging

Tomotaka Oroguchi, Masayoshi Nakasako

Physical Review E 87 （ 2 ） 022712 2013年02月

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)

MD-SAXS method with nonspherical boundaries

Tomotaka Oroguchi, Mitsunori Ikeguchi

Chemical Physics Letter 541   117 - 121 2012年07月

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)

Towards the structural characterization of intrinsically disordered proteins by SAXS and MD simulation

Tomotaka Oroguchi, Mitsunori Ikeguchi, Mamoru Sato

Journal of Physics: Conference Series 272 （ 1 ） 012005 2011年

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)

Fission yeast Swi5-Sfr1 protein complex, an activator of Rad51 recombinase, forms an extremely elongated dogleg-shaped structure

Yoichi Kokabu, Yasuto Murayama, Naoyuki Kuwabara, Tomotaka Oroguchi, Hiroshi Hashimoto, Yasuhiro Tsutsui, Naohito Nozaki, Satoko Akashi, Satoru Unzai, Toshiyuki Shimizu, Hitoshi Iwasaki, Matmoru Sato, Mitsunori Ikeguchi

Journal of Biological Chemistry 286 （ 50 ） 43569 - 43576 2011年12月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Mechanism of the conformational change of the F1-ATPase beta subunit revealed by free energy simulations

Yoko Ito, Tomotaka Oroguchi, Mitsunori Ikeguchi

Journal of American Chemical Society 133 （ 10 ） 3372 - 3380 2011年03月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

Tomotaka Oroguchi, Mitsunori Ikeguchi

Journal of Chemical Physics 134 （ 2 ） 025102 2011年01月

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)

Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms

Hiromasa Yagi, Hiroki Konno, Tomoe Murakami-Fuse, Atsuko Isu, Tomotaka Oroguchi, Hideo Akutsu, Mitsunori Ikeguchi, Toru Hisabori

Biochemical Journal 425 （ 1 ） 85 - 94 2010年01月

研究論文（学術雑誌）, 共著, 査読有り

• Access to Document (DOI)

Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics and X-ray scattering data analysis

Tomotaka Oroguchi, Hiroshi Hashimoto, Toshiyuki Shimizu, Mamoru Sato, Mitsunori Ikeguchi

Biophysical Journal 96 （ 7 ） 2808 - 2822 2009年04月

研究論文（学術雑誌）, 共著, 筆頭著者, 査読有り

• Access to Document (DOI)