研究者詳細 - 千見寺　浄慈

論文 - 千見寺　浄慈

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Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel <i>β</i>-sheet topologies 査読有り

Murata, H; Toko, K; Chikenji, G

PLOS COMPUTATIONAL BIOLOGY 20 巻 ( 8 ) 2024年8月

Exploration of novel & alpha;& beta;-protein folds through de novo design 査読有り国際誌

Minami Shintaro, Kobayashi Naohiro, Sugiki Toshihiko, Nagashima Toshio, Fujiwara Toshimichi, Tatsumi-Koga Rie, Chikenji George, Koga Nobuyasu

NATURE STRUCTURAL & MOLECULAR BIOLOGY 30 巻 ( 8 ) 頁： 1132 - + 2023年8月

The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold 招待有り査読有り

Nishina Takumi, Nakajima Megumi, Sasai Masaki, Chikenji George

MOLECULES 27 巻 ( 11 ) 2022年6月

The register shift rules for beta alpha beta-motifs for de novo protein design 査読有り

Murata Hiroto, Imakawa Hayao, Koga Nobuyasu, Chikenji George

PLOS ONE 16 巻 ( 8 ) 頁： e0256895 2021年

MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers 査読有り

Minami Shintaro, Sawada Kengo, Ota Motonori, Chikenji George

BIOINFORMATICS 34 巻 ( 19 ) 頁： 3324 - 3331 2018年10月

Exploring hydrophilic sequence space to search for uncharted foldable proteins by AlphaFold2 査読有り

Naoki Tomita, Hiroki Onoda, Leonard M. G. Chavas, George Chikenji

Biophysics and Physicobiology 22 巻 2025年2月

The cavity method to protein design problem 査読有り

Tomoei Takahashi, George Chikenji, Kei Tokita

Journal of Statistical Mechanics 2022 巻頁： 103403 2022年10月

Lattice protein design using Bayesian learning 査読有り

Takahashi Tomoei, Chikenji George, Tokita Kei

PHYSICAL REVIEW E 104 巻 ( 1 ) 2021年7月

Exploration of Novel Alpha-Beta Protein Folds by <i>De Novo</i> Design

Minami, S; Koga, R; Chikenji, G; Sugiki, T; Kobayashi, N; Koga, N

BIOPHYSICAL JOURNAL 118 巻 ( 3 ) 頁： 43A - 43A 2020年2月

A prospective compound screening contest identified broader inhibitors for Sirtuin 1 査読有り国際共著

Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

Scientific Reports 9 巻 ( 1 ) 頁： 19585 2019年12月

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Chiba Shuntaro, Ohue Masahito, Gryniukova Anastasiia, Borysko Petro, Zozulya Sergey, Yasuo Nobuaki, Yoshino Ryunosuke, Ikeda Kazuyoshi, Shin Woong-Hee, Kihara Daisuke, Iwadate Mitsuo, Umeyama Hideaki, Ichikawa Takaaki, Teramoto Reiji, Hsin Kun-Yi, Gupta Vipul, Kitano Hiroaki, Sakamoto Mika, Higuchi Akiko, Miura Nobuaki, Yura Kei, Mochizuki Masahiro, Ramakrishnan Chandrasekaran, Thangakani A. Mary, Velmurugan D., Gromiha M. Michael, Nakane Itsuo, Uchida Nanako, Hakariya Hayase, Tan Modong, Nakamura Hironori K., Suzuki Shogo D., Ito Tomoki, Kawatani Masahiro, Kudoh Kentaroh, Takashina Sakurako, Yamamoto Kazuki Z., Moriwaki Yoshitaka, Oda Keita, Kobayashi Daisuke, Okuno Tatsuya, Minami Shintaro, Chikenji George, Prathipati Philip, Nagao Chioko, Mohsen Attayeb, Ito Mari, Mizuguchi Kenji, Honma Teruki, Ishida Takashi, Hirokawa Takatsugu, Akiyama Yutaka, Sekijima Masakazu

SCIENTIFIC REPORTS 9 巻 2019年12月

Rules for connectivity of secondary structure elements in protein: Two-layer alpha beta sandwiches

Minami Shintaro, Chikenji George, Ota Motonori

PROTEIN SCIENCE 26 巻 ( 11 ) 頁： 2257 - 2267 2017年11月

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes 査読有り

Shuntaro Chiba, Takashi Ishida, Kazuyoshi Ikeda, Masahiro Mochizuki, Reiji Teramoto, Y-h Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, Michael Gromiha, Tatsuya Okuno, Koya Kato, Shintaro Minami, George Chikenji, Shogo D. Suzuki, Keisuke Yanagisawa, Woong-Hee Shin, Daisuke Kihara, Kazuki Yamamoto, Yoshitaka Moriwaki, Nobuaki Yasuo, Ryunosuke Yoshino, Sergey Zozulya, Petro Borysko, Roman Stavniichuk, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, and Masakazu Sekijima

Scientific Reports 7 巻頁： s41598-017-10275-4 2017年9月

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes

Chiba Shuntaro, Ishida Takashi, Ikeda Kazuyoshi, Mochizuki Masahiro, Teramoto Reiji, Taguchi Y-h., Iwadate Mitsuo, Umeyama Hideaki, Ramakrishnan Chandrasekaran, Thangakani A. Mary, Velmurugan D., Gromiha M. Michael, Okuno Tatsuya, Kato Koya, Minami Shintaro, Chikenji George, Suzuki Shogo D., Yanagisawa Keisuke, Shin Woong-Hee, Kihara Daisuke, Yamamoto Kazuki Z., Moriwaki Yoshitaka, Yasuo Nobuaki, Yoshino Ryunosuke, Zozulya Sergey, Borysko Petro, Stavniichuk Roman, Honma Teruki, Hirokawa Takatsugu, Akiyama Yutaka, Sekijima Masakazu

SCIENTIFIC REPORTS 7 巻 2017年9月

Rules for connectivity of secondary structure elements in protein: two-layer αβ sandwiches 査読有り

Shintaro Minami, George Chikenji, and Motonori Ota

Protein Science 26 巻 ( 11 ) 頁： 2257-2267 2017年8月

Importance of consensus region of multiple-ligand templates in a virtual screening method 査読有り

Tatsuya Okuno, Koya Kato, Shintaro Minami, Tomoki P. Terada, Masaki Sasai, George Chikenji

Biophysics and Physicobiology 13 巻頁： 149-156 2016年7月

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. 査読有り

S Chiba, K Ikeda, T Ishida, MM Gromiha, YH Taguchi, M Iwadate, H Umeyama, KY Hsin, H Kitano, K Yamamoto, N Sugaya, K Kato, T Okuno, G Chikenji, M Mochizuki, N Yasuo, R Yoshino, K Yanagisawa, T Ban, R Teramoto, C Ramakrishnan, AM Thangakani, D Velmurugan, P Prathipati, J Ito, Y Tsuchiya, K Mizuguchi, T Honma, T Hirokawa, Y Akiyama, M Sekijima

Scientific reports 5 巻頁： 17209 2015年11月

VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein-Ligand Complexes 査読有り

Tatsuya Okuno, Koya Kato, Tomoki P Terada, Masaki Sasai, George Chikenji

Journal of chemical information and modeling 55 巻 ( 6 ) 頁： 1108-1119 2015年6月

How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds 招待有り査読有り

Shintaro Minami, Kengo Sawada, George Chikenji

9 巻 ( 9 ) 頁： e107959 2014年9月

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments 査読有り

Shintaro Minami, Kengo Sawada, George Chikenji

BMC Bioinformatics 14 巻頁： 24 2013年1月

記述言語：英語掲載種別：研究論文（学術雑誌）

Background

Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed.
Results

We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, Cα only models, Alternative alignments, and Non-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here.
Conclusions

MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool for automatically detecting non-trivial structural relationships of proteins, such as circular permutations and segment-swapping, many of which have been identified manually by human experts so far. The source code of MICAN is freely download-able at http://www.tbp.cse.nagoya-u.ac.jp/MICAN.

DOI： 10.1186/1471-2105-14-24

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