構造データと分子シミュレーション技術によるインシリコ創薬支援研究
広川貴次(産業技術総合研究所　創薬分子プロファイリング研究センター)
アンサンブル、分子シミュレーション研究会,19 巻 4 号 225 頁～ 229 頁,DOI:https://doi.org/10.11436/mssj.19.225

Fibronectin type III domain-containing protein 5 interacts with APP and decreases amyloid production in Alzheimer's disease
Yasuha Noda(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University), Akira Kuzuya(Department of Neurology, Graduated School of Medicine, Kyoto University), Kyosuke Tanizawa(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University), Mitsugu Araki(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University), Ryoko Kawai(Department of Pharmaceuticals, Kyoto University), Biao Ma(Research and Development Group for in Silico Drug Discovery, Pro-Cluster Kobe, Foundation for Biomedical Research and Innovation(FBRI)), Yoko Sasakura(Research and Development Group for in Silico Drug Discovery, Pro-Cluster Kobe, Foundation for Biomedical Research and Innovation(FBRI)), Masato Maesako(Neurology of Alzheimer's Disease Laboratory, Massachusetts General Hospital, Harvard Medical School), Yoshitaka Tashiro(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University), Masakazu Miyamoto(Department of Neurology, Graduated School of Medicine, Kyoto University), Kengo Uemura(Department of Neurology, Graduated School of Medicine, Kyoto University), Yasushi Okuno(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University), Ayae Kinoshita(Department of Human Health Sciences, Graduated School of Medicine, Kyoto University)
Moleccular Brain,(2018) 11:61,DOI:10.1186/s13041-018-0401-8

A secondary RET mutation in the activation loop conferring resistance to vandetanib
Takashi Nakaoku(National Cancer Center Research Institute), Takashi Kohno(National Cancer Center Research Institute, National Cancer Center), Mitsugu Araki(RIKEN, Kyoto-University), Seiji Niho(National Cancer Center Hospital East), Rakhee Chauhan(The Francis Crick Institute, London), Phillip P. Knowles(The Francis Crick Institute, London), Katsuya Tsuchihara(National Cancer Center), Shingo Matsumoto(National Cancer Center, National Cancer Center Hospital East), Yoko Shimada(National Cancer Center Research Institute), Sachiyo Mimaki(National Cancer Center Hospital East), Genichiro Ishii(National Cancer Center), Hitoshi Ichikawa(National Cancer Center), Satoru Nagatoishi(The University of Tokyo), Kouhei Tsumoto(The University of Tokyo), Yasushi Okuno(Kyoto University), Kiyotaka Yoh(National Cancer Center Hospital East), Neil Q. McDonald(The Francis Crick Institute, London; Birkbeck College,London), Koichi Goto(National Cancer Center Hospital East)
Nature Communicationsvolume 9, Article number: 625 (2018) ,DOI:10.1038/s41467-018-02994-7

Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods
Ryoko Kawai(GraduateSchool of Pharmaceutical Sciences, Kyoto University, 46-29 YoshidaShimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan), Mitsugu Araki(GraduateSchool of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan; RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN), Masashi Yoshimura(GraduateSchool of Pharmaceutical Sciences, Kyoto University, 46-29 YoshidaShimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan), Narutoshi Kamiya(GraduateSchool of Simulation Studies, University of Hyogo, 7-1-28 MinatojimaMinami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan), Masahiro Ono(GraduateSchool of Pharmaceutical Sciences, Kyoto University, 46-29 YoshidaShimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan), Hideo Saji(GraduateSchool of Pharmaceutical Sciences, Kyoto University, 46-29 YoshidaShimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan), Yasushi Okuno(GraduateSchool of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan; RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN)
ACS Chemical Neuroscience,2018 May 16;9(5):957-966,DOI:10.1021/acschemneuro.7b00389

RNA inverse folding using Monte Carlo tree search
Xiufeng Yang(University of Tokyo), Kazuki Yoshizoe(University of Tokyo), Akito Taneda(Hirosaki University), Koji Tsuda(University of Tokyo)
BMC Bioinformatics,Vol.18, 468 (2017),DOI:10.1186/s12859-017-1882-7

ChemTS: an efficient python library for de novo molecular generation
Xiufeng Yang(Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.), Jinzhe Zhang(Department of Biosciences, INSA Lyon, Villeurbanne Cedex, France.), Kazuki Yoshizoe(RIKEN, Center for Advanced Intelligence Project, Tokyo, Japan.), Kei Terayama(Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.), Koji Tsuda(Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.; RIKEN, Center for Advanced Intelligence Project, Tokyo, Japan.; National Institute for Materials Science, Tsukuba, Japan.)
Science and Technology of Advanced Materials,Vol.18, pp.972-976 (2017),DOI:10.1080/14686996.2017.1401424

Machine learning accelerates MD-based binding pose prediction between ligands and proteins
Kei Terayama(Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan), Hiroaki Iwata(Foundation for Biomedical Research and Innovation, Hyogo 650-0047, Japan), Mitsugu Araki(RIKEN Advanced Institute for Computational Science, Hyogo 650-0047, Japan), Yasushi Okuno(RIKEN Advanced Institute for Computational Science, Hyogo 650-0047, Japan; Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan), Koji Tsuda(Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan; Center for Materials Research by Information Integration, NIMS, Ibaraki 305-0047, Japan; RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan)
Bioinformatics,Vol.34, pp.770-778 (2017),DOI:10.1093/bioinformatics/btx638

創薬におけるAIの可能性
種石　慶(理化学研究所), 岩田浩明、小島諒介、奥野恭史(京都大学)
日本化学会情報化学部会誌,35(3), 212, 2017, 10月号

臨床ビッグデータ解析の展望─実臨床データとゲノム情報への応用
内野詠一郎、中津井雅彦、鎌田真由美、荒木望嗣、奥野恭史(京都大学), 種石　慶(理化学研究所)
日本エム・イー学会誌「生体医工学」,55(4):173-182,2017.

Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Yuta Shinohara(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Yohei M. Koyama(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Maki Ukai-Tadenuma(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Takatsugu Hirokawa(Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST)), Masaki Kikuchi(Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies), Rikuhiro G. Yamada(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Hideki Ukai(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Hiroshi Fujishima(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center), Takashi Umehara(Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies), Kazuki Tainaka(Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo), Hiroki R. Ueda(Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center)
Molecular Cell,Vol.67, pp.783-798.e20 (2017),DOI:10.1016/j.molcel.2017.08.009

CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning
Hamanaka, M(Kyoto University), Tanaishi, Kei(RIKEN), Iwata, H(Foundation for Biomedical Research and Innovation), Ye, J(Intel Corporation), Pei, J(Intel Corporation), Hou, J(Intel Corporation), Okuno, Y(Kyoto University)
Molecular Informatics,36(1-2), 2017,DOI:10.1002/minf.201600045

Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor
Bekker, G(Osaka University), Kamiya, N(Osaka University, RIKEN, University of Hyogo), Araki, M(RIKEN, Kyoto University), Fukuda, I(Osaka University), Okuno, Y(RIKEN, Kyoto University), Nakamura, H(Osaka University)
Journal of Chemical Theory and Computation ,13(6), 2389－2399, 2017.,DOI:10.1021/acs.jctc.6b01127

Association between UGT1A1*28*28 genotype and lung cancer in the Japanese population
Nishikawa, Y(Kyoto University), Kanai, M(Kyoto University), Narahara, M(Kyoto University, McGill University), Tamon, A(Kyoto University), Brown, J.B.(Kyoto University), Taneishi, K(RIKEN), Nakatsui, M.(Kyoto University), Okamoto, K(Kyoto University Hospital), Uneno, Y(Kyoto University), Yamaguchi, D(Kyoto University), Tomono, T(Kyoto University), Mori, Y(Kyoto University), Matsumoto, S(Kyoto University), Okuno, Y(Kyoto University), Muto, M(Kyoto University)
INTERNATIONAL JOURNAL OF CLINICAL ONCOLOGY,22-2, 269-273(2017) ,DOI:10.1007/s10147-016-1061-2

Brigatinib combined with anti-EGFR antibody overcomes osimertinib resistance in EGFR-mutated non-small-cell lung cancer
Ken Uchibori(Japanese Foundation for Cancer Research), Naohiko Inase(Tokyo Medical and Dental University), Mitsugu Araki(RIKEN), Mayumi Kamada(Kyoto University), Shigeo Sato(Japanese Foundation for Cancer Research), Yasushi Okuno(RIKEN, Kyoto University), Naoya Fujita(Japanese Foundation for Cancer Research), Ryohei Katayama(Japanese Foundation for Cancer Research)
Nature Communications, 8, Article number: 14768 (2017) ,DOI:10.1038/ncomms14768

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
Mitsugu Araki(RIKEN Advanced Institute for Computational Science), Narutoshi Kamiya(Graduate School of Simulation Studies, University of Hyogo), Miwa Sato(Mitsui Knowledge Industry Co., Ltd.), Masahiko Nakatsui(Graduate School of Medicine, Kyoto University), Takatsugu Hirokawa(Division of Biomedical Science, Faculty of Medicine, University of Tsukuba), Yasushi Okuno(Graduate School of Medicine, Kyoto University)
Journal of Chemical Information and Modeling,Vol.56, 12, pp2445-2456,DOI:10.1021/acs.jcim.6b00398

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
David A. duVerle(University of Tokyo), Sohiya Yotsukura(Kyoto University), Seitaro Nomura(University of Tokyo), Hiroyuki Aburatani(University of Tokyo), Koji Tsuda(University of Tokyo)
BMC Bioinformatics, Vol.17, 363 (2016),DOI:10.1186/s12859-016-1175-6

COMBO: An efficient Bayesian optimization library for materials sciencer
Tsuyoshi Ueno(Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5-CB02 Kashiwanoha, Kashiwa 277-8561, Japan), Trevor David Rhone(Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA), Zhufeng Hou(Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan), Teruyasu Mizoguchi(Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo 153-8505, Japan), Koji Tsuda(Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5-CB02 Kashiwanoha, Kashiwa 277-8561, Japan, Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan)a
Materials Discovery, Volume 4, Pages 18-21 (2016) ,DOI:10.1016/j.md.2016.04.001