Journal Paper

• Daiki Erikawa, Nobuaki Yasuo, Takamasa Suzuki, Shogo Nakamura, Masakazu Sekijima. Gargoyles: An Open Source Graph-Based Molecular Optimization Method Based on Deep Reinforcement Learning, ACS Omega, Sept. 2023.  Official location  
• Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, Masakazu Sekijima. Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography, ACS omega, Vol. 8, No. 29, pp. 25850-25860, July 2023.
• Ryo Nakayama, Ryota Shimizu, Taishi Haga, Takefumi Kimura, Yasunobu Ando, Shigeru Kobayashi, Nobuaki Yasuo, Masakazu Sekijima, Taro Hitosugi. Tuning of Bayesian optimization for materials synthesis: simulation of the one-dimensional case, Science and Technology of Advanced Materials: Methods, Dec. 2022.  Official location  
• Nurkanto Arif, Riyo Imamura, Yulia Rahmawati, Erwahyuni Endang Prabandari, Danang Waluyo, Takeshi Annoura, Kazuki Yamamoto, Masakazu Sekijima, Yuki Nishimura, Takayoshi Okabe, Tomoo Shiba, Norio Shibata, Hirotatsu Kojima, James Duffy, Tomoyoshi Nozaki. Dephospho-Coenzyme A Kinase Is an Exploitable Drug Target against Plasmodium falciparum: Identification of Selective Inhibitors by High-Throughput Screening of a Large Chemical Compound Library, Antimicrobial Agents and Chemotherapy, Oct. 2022.  Official location  
• Junya Tabata, Takashi Nakaoku, Mitsugu Araki, Ryunosuke Yoshino, Shinji Kohsaka, Ayaka Otsuka, Masachika Ikegami, Ayako Ui, Shin-ichiro Kanno, Keiko Miyoshi, Shigeyuki Matsumoto, yukari sagae, Akira Yasui, Masakazu Sekijima, Hiroyuki Mano, Yasushi Okuno, Aikou Okamoto, Takashi Kohno. Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis, Cancer Research, Vol. 82, No. 20, pp. 3751-3762, Oct. 2022.  Official location  
• Kazuki Takeda, Kosuke Manago, Ayuko Morita, Yusuke K. Kawai, Nobuaki Yasuo, Masakazu Sekijima, Yoshinori Ikenaka, Takuma Hashimoto, Ryuichi Minato, Yusuke Oyamada, Kazuo Horikoshi, Hajime Suzuki, Mayumi Ishizuka, Shouta M.M. Nakayama. Toxicokinetic analysis of the anticoagulant rodenticides warfarin & diphacinone in Egyptian fruit bats (Rousettus aegyptiacus) as a comparative sensitivity assessment for Bonin fruit bats (Pteropus pselaphon), Ecotoxicology and Environmental Safety, Vol. 243, pp. 113971, Sept. 2022.  Official location  
• R Prabakaran, Puneet Rawat, Nobuaki Yasuo, Masakazu Sekijima, Sandeep Kumar, Gromiha Michael. Effect of charged mutation on aggregation of a pentapeptide: Insights from molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics, Vol. 90, No. 2, pp. 405-417, Feb. 2022.  Official location  
• Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig. Statistical potentials for RNA-protein interactions optimized by CMA-ES, Journal of Molecular Graphics and Modelling, Jan. 2022.  Official location  
• Kazuki Z Yamamoto, NOBUAKI YASUO, Masakazu Sekijima. Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides, Journal of Chemical Information and Modeling, Vol. 62, No. 2, pp. 350-358, Jan. 2022.  Official location  
• Masakazu Sekijima, Masakazu Sekijima. MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning, Journal of Cheminformatics, Vol. 13, No. 1, Dec. 2021.  Official location  
• Nobuaki Yasuo, Takashi Ishida, Masakazu Sekijima. Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project, Aug. 2021.
• Nobuaki Yasuo, Takashi Ishida, Masakazu Sekijima. Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project, Parasitology International, Vol. 83, pp. 102366, Aug. 2021.  Official location  
• Rajib Acharjee, Keith Talaam, Endah D. Hartuti, Yuichi Matsuo, Takaya Sakura, Bundutidi M. Gloria, Shinya Hidano, Yasutoshi KIDO, Mihoko Mori, Kazuro Shiomi, Masakazu Sekijima, Tomoyoshi Nozaki, Kousuke Umeda, yoshifumi nishikawa, Shinjiro Hamano, Kiyoshi Kita, Daniel Ken INAOKA. Biochemical Studies of Mitochondrial Malate: Quinone Oxidoreductase from Toxoplasma gondii, International Journal of Molecular Sciences, July 2021.  Official location  
• Masakazu Sekijima. Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding, Proteins: Structure, Function, and Bioinformatics, Apr. 2021.  Official location  
• Masakazu Sekijima. Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates, Scientific Reports, Vol. 10, No. 1, Dec. 2020.  Official location  
• Masakazu Sekijima. Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates, Scientific Reports, Vol. 10, No. 1, Dec. 2020.  Official location  
• Yu Miyazaki, Ryo Nakayama, Nobuaki Yasuo, Yuki Watanabe, Ryota Shimizu, Daniel M. Packwood, Kazunori Nishio, Yasunobu Ando, Masakazu Sekijima, Taro Hitosugi. Bayesian statistics-based analysis of AC impedance spectra, AIP Advances, Apr. 2020.  Official location  
• Misa Sayama, Akiharu Uwamizu, Yuko Otani, Asuka Inoue, Junken Aoki, Masakazu Sekijima, Tomohiko Ohwada. Membrane Phospholipid Analogues as Molecular Rulers to Probe the Position of the Hydrophobic Contact Point of Lysophospholipid Ligands on the Surface of G-Protein-Coupled Receptor during Membrane Approach, Biochemistry, Vol. 59, No. 11, pp. 1173-1201, Mar. 2020.  Official location  
• Masakazu Sekijima. Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil, Scientific Reports, Dec. 2019.  Official location  
• Masakazu Sekijima. A prospective compound screening contest identified broader inhibitors for Sirtuin 1, Scientific Reports, Dec. 2019.  Official location  
• Ryunosuke Yoshino, Nobuaki Yasuo, Masakazu Sekijima. Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil, Scientific Reports, Dec. 2019.  Official location  
• 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 Nakamura, Shogo Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki 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.. A prospective compound screening contest identified broader inhibitors for Sirtuin 1, Scientific Reports, 9, Dec. 2019.  Official location  
• Sherlyn Jemimah, Masakazu Sekijima, Michael Gromiha. ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification, Bioinformatics, Nov. 2019.  Official location  
• Masakazu Sekijima. ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification, Bioinformatics, Nov. 2019.  Official location  
• Shintaro Sengoku, Masakazu Sekijima, Koichiro Iha, Reiko Onodera. AI/ビッグデータ，ICT と医薬品 ─ 知財・標準の側面から, 仙石慎太郎, 関嶋政和, 伊波興一朗, 小野寺玲子, Vol. 16, No. 1, pp. 58-64, June 2019.
• Nobuaki Yasuo, Masakazu Sekijima. Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning, Journal of Chemical Information and Modeling, Vol. 59, No. 3, pp. 1050-1061, Mar. 2019.  Official location  
• Nobuaki Yasuo, Masakazu Sekijima. Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning, Journal of Chemical Information and Modeling, Vol. 59, No. 3, pp. 1050-1061, Mar. 2019.  Official location  
• Masakazu Sekijima. CoDe-DTI: Collaborative Deep Learning-based Drug-Target Interaction Prediction, Dec. 2018.  Official location  
• Nobuaki Yasuo, Yusuke Nakashima, Masakazu Sekijima. CoDe-DTI: Collaborative Deep Learning-based Drug-Target Interaction Prediction, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Dec. 2018.  Official location  
• Wakui, N., Yoshino, R., Yasuo, N., Ohue, M., Sekijima, M.. Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach, Journal of Molecular Graphics and Modelling, Vol. 79, pp. 166-174, Jan. 2018.  Official location  
• Ramakrishnan C, Thangakani AM, Velmurugan D, Krishnan DA, Sekijima M, Akiyama Y, Gromiha MM.. Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques, Journal of Biomolecular Structure and Dynamics, Volume 36, Issue 6, Page 1566-1576, 2018.
• Wakui N, Yoshino R, Yasuo N, Ohue M, Sekijima M. Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach., Journal of molecular graphics & modelling, Nov. 2017.  Official location  
• Shuntaro Chiba, Takashi Ishida, Kazuyoshi Ikeda, Masahiro Mochizuki, Reiji Teramoto, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Tatsuya Okuno, Koya Kato, Shintaro Minami, George Chikenji, Shogo D. Suzuki, Keisuke Yanagisawa, Woong-Hee Shin, Daisuke Kihara, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Nobuaki Yasuo, Ryunosuke Yoshino, Sergey Zozulya, Petro Borysko, Roman Stavniichuk, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima. An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes, Scientific Reports, Nature Publishing Group, Vol. 7, No. 12038, pp. 1-13, Sept. 2017.
• Masakazu Sekijima. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease., Scientific reports, July 2017.  Official location  
• Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, Masakazu Sekijima. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease, Scientific Reports, Springer Nature, 7, July 2017.
• Masakazu Sekijima. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease., Scientific reports, July 2017.  Official location  
• Masakazu Sekijima. Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques., Journal of biomolecular structure & dynamics, June 2017.  Official location  
• Shuntaro Chiba, Kazuyoshi Ikeda, Takashi Ishida, M. Michael Gromiha, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Kun-Yi Hsin, Hiroaki Kitano, Kazuki Yamamoto, Nobuyoshi Sugaya, Koya Kato, Tatsuya Okuno, George Chikenji, Masahiro Mochizuki, Nobuaki Yasuo, Ryunosuke Yoshino, Keisuke Yanagisawa, Tomohiro Ban, Reiji Teramoto, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, Philip Prathipati, Junichi Ito, Yuko Tsuchiya, Kenji Mizuguchi, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima. Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target, Scientific Reports, Vol. 5, No. 17209, Nov. 2015.
• Ryunosuke Yoshino, Nobuaki Yasuo, Daniel Ken Inaoka, Yohsuke Hagiwara, Kazuki Ohno, Masaya Orita, Masayuki Inoue, Tomoo Shiba, Shigeharu Harada, Teruki Honma, Emmanuel Oluwadare Balogun, Josmar Rodrigues da Rocha, Carlos Alberto Montanari, Kiyoshi Kita, Masakazu Sekijima. Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method, PLOS ONE, May 2015.  Official location  
• Nagarajan R, Chothani SP, Ramakrishnan C, Sekijima M, Gromiha MM. Structure based approach for understanding organism specific recognition of protein-RNA complexes., 2015.  Official location  
• Chiba S, Ikeda K, Ishida T, Gromiha MM, Taguchi YH, Iwadate M, Umeyama H, Hsin KY, Kitano H, Yamamoto K, Sugaya N, Kato K, Okuno T, Chikenji G, Mochizuki M, Yasuo N, Yoshino R, Yanagisawa K, Ban T, Teramoto R, Masakazu Sekijima. Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target., 2015.  Official location  
• Nagarajan R, Chothani SP, Ramakrishnan C, Sekijima M, Gromiha MM. Structure based approach for understanding organism specific recognition of protein-RNA complexes., 2015.  Official location  
• Yoshino R, Yasuo N, Inaoka DK, Hagiwara Y, Ohno K, Orita M, Inoue M, Shiba T, Harada S, Honma T, Balogun EO, da Rocha JR, Montanari CA, Kita K, Sekijima M. Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method., 2015.  Official location  
• Hagiwara Y, Ohno K, Orita M, Koga R, Endo T, Akiyama Y, Sekijima M. Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery., Sept. 2013.  Official location  
• Hagiwara Y, Ohno K, Orita M, Koga R, Endo T, Akiyama Y, Sekijima M.. Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery, Curr Comput Aided Drug Des. 2013, Vol. 9, No. 3, pp. 396-401, Sept. 2013.
• Hagiwara Y, Ohno K, Orita M, Koga R, Endo T, Akiyama Y, Sekijima M. Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery., Sept. 2013.  Official location  
• Takano R, Kiso M, Igarashi M, Le QM, Sekijima M, Ito K, Takada A, Kawaoka Y. Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses., Jan. 2013.  Official location  
• Ryo Takano, Maki Kiso, Manabu Igarashi, Quynh Mai Le, Masakazu Sekijima, Ito Kimihito, Ayato Takada, Yoshihiro Kawaoka. Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the NA of H5N1 avian influenza viruses, Journal of Infectious Diseases, Infectious Diseases Society of America, Oct. 2012.  Official location  
• Saito S, Ohno K, Sekijima M, Suzuki T, Sakuraba H. Database of the clinical phenotypes, genotypes and mutant arylsulfatase B structures in mucopolysaccharidosis type VI., Apr. 2012.  Official location  
• Saito S, Ohno K, Sekijima M, Suzuki T, Sakuraba H. Database of the clinical phenotypes, genotypes and mutant arylsulfatase B structures in mucopolysaccharidosis type VI., Apr. 2012.  Official location  
• Seiji Saito, Kazuki Ohno, Masakazu Sekijima, Toshihiro Suzuki, Hitoshi Sakuraba. Database of the clinical phenotypes, genotypes and mutant arylsulfatase B structures in mucopolysaccharidosis type VI, Journal of Human Genetics, Nature Publishing Group, Vol. 57, pp. 280-282, Apr. 2012.  Official location  
• Takahiro Shinozaki, Toshinao Iwaki, Shiqiao Du, Masakazu Sekijima, Sadaoki Furui. Distance-based factor graph linearization and sampled max-sum algorithm for efficient 3D potential decoding of macromolecules, IPSJ Transaction on Bioinformatics, Vol. 4, pp. 34-44, Dec. 2011.
• Mayumi Kamada, Mikito Toda, Masakazu Sekijima, Masami Takata, Kazuki Joe. Analysis of motion features for molecular dynamics simulation of proteins, Chemical Physics Letters, Vol. 502, pp. 241-247, Jan. 2011.
• Sugawara K, Saito S, Sekijima M, Ohno K, Tajima Y, Kroos MA, Reuser AJ, Sakuraba H. Structural modeling of mutant alpha-glucosidases resulting in a processing/transport defect in Pompe disease., June 2009.  Official location  
• Sugawara K, Saito S, Sekijima M, Ohno K, Tajima Y, Kroos MA, Reuser AJ, Sakuraba H. Structural modeling of mutant alpha-glucosidases resulting in a processing/transport defect in Pompe disease., June 2009.  Official location  
• Honda S, Akiba T, Kato YS, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T, Harata K. Crystal structure of a ten-amino acid protein., Nov. 2008.  Official location  
• Honda S, Akiba T, Kato YS, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T, Harata K. Crystal structure of a ten-amino acid protein., Nov. 2008.  Official location  
• Sekijima M, Motono C, Yamasaki S, Kaneko K, Akiyama Y. Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties., Aug. 2003.  Official location  
• Sekijima M, Motono C, Yamasaki S, Kaneko K, Akiyama Y. Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties., Aug. 2003.  Official location  

International Conference (Reviewed)

• Hayato Fujita, Akihiro Nomura, Toshio Endo, Masakazu Sekijima. Enhancing the Performance of AlphaFold Through Modified Storage Method and Optimization of HHblits on TSUBAME3.0 Supercomputer, 2023 Congress in Computer Science, Computer Engineering, & Applied Computing (CSCE), proceedings of 2023 Congress in Computer Science, Computer Engineering, & Applied Computing (CSCE), July 2023.
• Mami Ozawa, Nobuaki Yasuo, Masakazu Sekijima. An Improved Model for Predicting Compound Retrosynthesizability Using Machine Learning, 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE), Nov. 2022.  Official location  
• Shiqiao Du, Takuro Udagawa, Toshio Endo, Masakazu Sekijima. Molecular Dynamics Simulation of a Biomolecule with High Speed, Low Power and Accuracy Using GPU-Accelerated TSUBAME2.0 Supercomputer, Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC 2011), Proceedings of Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC 2011), Dec. 2011.
• Takahiro Shinozaki, Masakazu Sekijima, Shigeki Hagihara, Sadaoki Furui. Compact speech decoder based on pure functional programming, APSIPA ASC 2011, Proc. APSIPA ASC 2011, Oct. 2011.
• Takuro Udagawa, Masakazu Sekijima. Energy Consumption of GPU with Molecular Dynamics, the 22th IASTED International Conference on Parallel and Distributed Computing and Systems, Proceedings of the 22th IASTED International Conference on Parallel and Distributed Computing and Systems, ACTA Press, Nov. 2010.  Official location  

International Conference (Not reviewed / Unknown)

• Naoki Wakui, Ryunosuke Yoshino, Nobuaki Yasuo, Masahito Ohue, Masakazu Sekijima. Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simiulation approach, 4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design, Nov. 2017.  Official location  
• Takaaki Sasaki, Masakazu Sekijima. Development of Protein Ligand Binding Site Prediction System by Dynamics of Water Molecules, Biophysical Society 56th Annual Meeting, Biophysical Society 56th Annual Meeting Program, Biophysical Society, Feb. 2012.  Official location  
• N. Inose, T. Shinozaki, S. Du, S. Furui, M. Sekijima. Protein Potential Energy Minimization Using Slice Chain Max-Sum Algorithm, 26th Annual Symposium of The Protein Society, 2012.  Official location  
• Yusuke Matsuzaki, Yuri Matsuzaki, Masakazu Sekijima, Yutaka Akiyama. Protein structure sampling based on molecular dynamics and improvement of docking prediction, BIOINFO 2009 CBI-KSBSB Joint Conference, Proc. BIOINFO 2009 CBI-KSBSB Joint Conference, P10-99, Nov. 2009.
• Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama. Binding analysis of neuraminidase inhibitors by fragment MO calculation, BIOINFO 2009 CBI-KSBSB Joint Conference, Proc. BIOINFO 2009 CBI-KSBSB Joint Conference, P7-74, Nov. 2009.

Domestic Conference (Not reviewed / Unknown)

• Hayato Fujita, Akihiro Nomura, Toshio Endo, Masakazu Sekijima. タンパク質立体構造予測システム AlphaFold の TSUBAME3.0 上での高速化, 情報処理学会 第183回ハイパフォーマンスコンピューティング研究発表会, 情報処理学会研究報告, Vol. 2022-HPC-183, No. 3, pp. 1--7, Mar. 2022.
• 中山 亮, Ryota Shimizu, Taishi Haga, Takefumi Kimura, 安藤 康伸, Nobuaki Yasuo, Masakazu Sekijima, Taro Hitosugi. 物質合成に適したベイズ最適化のハイパーパラメータの探索, 第68回応用物理学会春季学術講演会, Mar. 2021.
• 千葉 真人, Masami Sako, Yoshihiro Hayashi, SHINJI ANDO, Nobuaki Yasuo, Masakazu Sekijima, Susumu Kawauchi. 量子化学計算と機械学習による有機高分子の屈折率予測, 高分子学会, 高分子学会予稿集, Vol. 69, No. 2, p. 2G12, Sept. 2020.
• Masami Sako, 千葉 真人, Nobuaki Yasuo, 渡部 一貴, 瀧本 啓人, Taro Hitosugi, Masakazu Sekijima. Pb-free perovskite 化合物の bandgap 予測と合成結果, 第81回応用物理学会秋季学術講演会, Sept. 2020.
• 中山 亮, Yu Miyazaki, Nobuaki Yasuo, Yuki Watanabe, Ryota Shimizu, Kazunori Nishio, 安藤 康伸, Masakazu Sekijima, Taro Hitosugi. ベイズ統計に基づいた単純な電気化学素子のインピーダンススペクトル解析, 第67回応用物理学会春季学術講演会, Mar. 2020.
• Yu Miyazaki, Nobuaki Yasuo, Yuki Watanabe, 中山 亮, Ryota Shimizu, Kazunori Nishio, 安藤 康伸, Masakazu Sekijima, Taro Hitosugi. ベイズ推定を用いた客観的な電気化学インピーダンス解析, 電気化学会第86回大会, Mar. 2019.
• Yu Miyazaki, Nobuaki Yasuo, Yuki Watanabe, 中山 亮, Ryota Shimizu, Kazunori Nishio, 安藤 康伸, Masakazu Sekijima, Taro Hitosugi. ベイズ統計を用いた客観的な電気化学インピーダンススペクトル解析, 第66回応用物理学会春季学術講演会, Mar. 2019.
• Takahiro Shinozaki, Masakazu Sekijima. SCMS2.0によるタンパク質ポテンシャルエネルギー最小化の諸条件における評価, バイオ情報学研究発表会, Mar. 2014.
• Norikazu Sugiura, Takashi Ishida, Yutaka Akiyama, Masakazu Sekijima. de Bruijn Graphの分割によるVelvetの消費メモリの低減, 第36回バイオ情報学研究会, 情報処理学会研究報告, vol. 2013-BIO-36, no. 6, pp. 1-7, Dec. 2013.
• Yuuki Saitou, Takashi Ishida, Masakazu Sekijima, Yutaka Akiyama. 結合自由エネルギー予測を用いたクリアランス経路予測の改善に関する研究, 第34回バイオ情報学研究会, 情報処理学会研究報告, vol. 2013-BIO-34, no. 15, pp. 1-6, June 2013.
• Shunsuke Yoshikawa, Takashi Ishida, Masakazu Sekijima, Yutaka Akiyama. Sparse k-mer graphアルゴリズムの評価とVelvetへの実装, 第34回バイオ情報学研究会, 情報処理学会研究報告, vol. 2013-BIO-34, no. 1, pp. 1-7, June 2013.
• Sugiura Norikazu, Ishida Takashi, Sekijima Masakazu, Akiyama Yutaka. De novo sequence assembly based on divided hash tables, 情報処理学会第29回バイオ情報学研究発表会, IPSJ SIG Technical Report, 情報処理学会, 2012-BIO-29, June 2012.
• Naoto Inose, Takahiro Shinozaki, Shiqiao Du, Sadaoki Furui, Masakazu Sekijima. A study on the potential energy minimization of proteins by Slice Chain Max-Sum algorithm, 情報処理学会バイオ情報学研究会, Vol. 2012-BIO-28, No. 20, pp. 1-8, Mar. 2012.
• Kana Fuji, Masakazu Sekijima, Hiroshi Fujisaki, Mikito Toda. 生体分子の分子動力学に対する時系列解析ー集団運動の揺らぎと構造変化の関係を探るー, 第50回日本生物物理学会年会, 生物物理, 日本生物物理学会, Vol. 52, Supplement1, 2012.
• Kana Fuji, Masakazu Sekijima, Hiroshi Fujisaki, Mikito Toda. 生体分子の分子動力学に対する時系列解析ー集団運動の揺らぎと構造変化の関係を探るーII, 日本物理学会 2012年秋季大会, 2012.  Official location  
• Kana Fuji, Masakazu Sekijima, Mikito Toda. 分子動力学の時系列データ解析ー側鎖の構造変化と運動ー, 第49回日本生物物理学会, Sept. 2011.  Official location  
• Takahiro Shinozaki, Toshinao Iwaki, Shichao Du, Masakazu Sekijima, SADAOKI FURUI. Distance based Graph Linearization and Sampled Max-sum Algorithm for Efficient 3D Potential Decoding of Macromolecules, 情報処理学会第26回バイオ情報学研究発表会, 情報処理学会研究会報告, 2011-BIO-26, Sept. 2011.
• Takaaki Sasaki, Masakazu Sekijima. Ligand binding site prediction in protein by water molecule information entropy, The 11th Annual Meeting of the Protein Science Society of Japan, 第11回日本蛋白質科学会年会 プログラム・要旨集, pp. 130-130, May 2011.  Official location  
• Takahiro Shinozaki, Masakazu Sekijima, Shigeki Hagihara, Sadaoki Furui. A compact speech decoder based on pure functional programming, IPSJ-SIGPRO, Manuscript for presentation at IPSJ-SIGPRO, 25 April 2011., 2010-5, 6, Apr. 2011.
• Takahiro Shinozaki, Masakazu Sekijima, Shigeki Hagihara, SADAOKI FURUI. 純粋関数型言語を用いた超コンパクトデコーダの開発, 情報処理学会, Apr. 2011.
• Takaaki Sasaki, Masakazu Sekijima. 情報エントロピーによるタンパク質のリガンド結合部位予測, 情報処理学会第73回全国大会, Mar. 2011.
• Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama. タンパク質-リガンド間の結合性解析の自動パイプライン化, 情報処理学会 第73回全国大会, Mar. 2011.
• Takurou Udagawa, Masakazu Sekijima. 分子動力学法のマルチノード環境におけるGPUの電力効率の評価, 情報処理学会第73回全国大会, Mar. 2011.  Official location  
• Takaaki Sasaki, Masakazu Sekijima. タンパク質内の水分子のダイナミクス解析によるリガンド結合部位予測, 情報処理学会 第23回バイオ情報学研究会, IPSJ SIG Technical Report, 情報処理学会, Vol. 2010-BIO-23, No. 31, pp. 1-4, Dec. 2010.
• Takurou Udagawa, Masakazu Sekijima. Energy Consumption and Acceleration of GPU of Molecular Dynamics Simulation, 情報処理学会 第127回ハイパフォーマンスコンピューティング研究会, IPSJ SIG Technical Report, 情報処理学会, Vol. Vol.2010-HPC-127, No. 5, pp. 1-5, Oct. 2010.  Official location  
• Takahiro Shinozaki, Masakazu Sekijima, Shigeki Hagihara, SADAOKI FURUI. 柔軟でコンパクトな純粋関数型デコーダの検討, 日本音響学会2010年秋季研究発表会, 日本音響学会2010年秋季講演論文集, 日本音響学会, No. 1-Q-26, pp. 181-182, Sept. 2010.
• Yusuke Matsuzaki, Masahito Ohue, Yuri Matsuzaki, Toshiyuki Sato, Masakazu Sekijima, Yutaka Akiyama. Improvement of rigid-body prediction for unbound docking based on protein feature, 情報処理学会 第20回バイオ情報学研究会, IPSJ SIG Technical Report, 情報処理学会, Vol. 2010-BIO-20, No. 4, pp. 1-8, Feb. 2010.  Official location  
• Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama. フラグメントMO法によるノイラミニダーゼ阻害薬の結合性解析, IPSJ SIG BIO, IPSJ SIG Technical Report, Information Processing Society of Japan, Vol. 2009-BIO-18, No. 4, pp. 1-7, Sept. 2009.
• Yusuke Matsuzaki, Yuri Matsuzaki, Masakazu Sekijima, Yutaka Akiyama. Protein structure sampling based on molecular dynamics and improvement of docking prediction, IPSJ SIG BIO, IPSJ SIG Technical Report, Information Processing Society of Japan, Vol. 2009-BIO-18,, No. 1, pp. 1-6, Sept. 2009.
• Masakazu Sekijima, 高崎 慎也, 中村 周吾, 池口 満徳, 清水 謙多郎. サブタスク間の依存関係に基づくスケジューリング機構を備えた並列プログラミング環境の開発, 情報処理学会論文誌プログラミング（PRO）, 一般社団法人情報処理学会, Vol. 41, No. 2, pp. 65-77, Feb. 2000.
• Masakazu Sekijima, Shinya Takasaki, 中村 周吾, 池口 満徳, 清水 謙多郎. サブタスク間の依存関係に基づくスケジューリング機構を備えた並列プログラミング環境の開発, 情報処理学会論文誌プログラミング（PRO）, 一般社団法人情報処理学会, Vol. 41, No. 2, pp. 65-77, Feb. 2000.

Patent

• Masakazu Sekijima, Gen Li, Nobuaki Yasuo. 化合物生成装置、化合物生成方法、学習装置、学習方法及びプログラム. Patent. Registered. 国立大学法人東京工業大学. 2020/03/31. 特願2020-063193. 2021/04/30. 特開2021-068410. 特許第7483244号. 2024/05/07 2024.
• Masakazu Sekijima, Hiroshi Yoda, Nobuaki Yasuo. 立体構造判定装置、立体構造判定方法、立体構造の判別器学習装置、立体構造の判別器学習方法及びプログラム. Patent. Registered. 国立大学法人東京工業大学. 2019/01/31. 特願2019-015086. 2020/08/13. 特開2020-123189. 特許第7168979号. 2022/11/01 2022.

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