Updated on 2026/03/06
Molecular simulation, Computational chemistry
2001.4 - 2003.9 The Graduate University for Advanced Studies
1999.4 - 2001.3 Kagoshima University
1995.4 - 1999.3 Kagoshima University
2026.2 Kagoshima University Research Field in Cooperation, Integrated Arts and Sciences Area Computing and Communications Center Associate Professor
2026.2 Okayama University
2020.9 - 2022.3 Nagoya University
2019.4 - 2026.1 高度情報科学技術研究機構 計算科学技術部 研究員
2017.5 - 2019.3 Temple University Department of Chemistry Assistant Professor
2014.4 - 2017.4 Nagoya University Assistant Professor
2013.6 - 2017.4 Nagoya University
2011.4 - 2014.3 自然科学研究機構分子科学研究所 研究員
2009.4 - 2011.3 Nagoya University Assistant Professor
2008.4 - 2009.3 自然科学研究機構分子科学研究所 研究員
2007.4 - 2008.3 Hiroshima University Assistant Professor
2004.4 - 2006.3 Hiroshima University Research Associate
2003.10 - 2004.3 Hiroshima University Research Assistant
2013.1 - 2014.12 Biophysical Society
2010.4 - 2011.3 日本蛋白質科学会
2005.4 日本生物物理学会
2011 溶液化学シンポジウム 実行委員 Academic society
2009 新学術領域「揺らぎと生体機能」第3階公開シンポジウム 実行委員 Academic society
2007 第4回ナノ・バイオ・インフォ化学シンポジウム 実行委員 Academic society
2007 情報計算化学生物学会（CBI学会）2007年大会 実行委員 Academic society
2006 第3回ナノ・バイオ・インフォ化学シンポジウム 実行委員 Academic society
2005 第2回ナノ・バイオ・インフォ化学シンポジウム 実行委員 Academic society
2004 第8回理論化学討論会 実行委員 Academic society
2004 第1回ナノ・バイオ・インフォ化学シンポジウム 実行委員 Academic society
2004 分子構造総合討論会2004 実行委員 Academic society
2016.1 - 2016.3 National Institutes of Health Visiting Researcher
2014.10 - 2015.1 The State University of New York at Stony Brook Visiting Researcher
Saeko Yanaka, Yoshitake Sakae, Yohei Miyanoiri, Takumi Yamaguchi, Yukiko Isono, Sachiko Kondo, Miyuki Iwasaki, Masayoshi Onitsuka, Hirokazu Yagi, Koichi Kato . Exploring Glycoform-Dependent Dynamic Modulations in Human Immunoglobulin G via Computational and Experimental Approaches . Proceedings of the National Academy of Sciences of the United States of America122 e2505473122 2025Reviewed
Yoshitake Sakae, Takeshi Kawasaki and Yuko Okamoto . Distribution and structure analysis of fibril-forming peptides focusing on concentration dependency . ACS Omega7 10012 - 10021 2022Reviewed
Yoshitake Sakae, Bin W Zhang, Ronald M Levy and Nanjie Deng . Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses . Journal of Computational Chemistry41 56 - 68 2020Reviewed International coauthorship
Yoshitake Sakae, John E. Straub and Yuko Okamoto . Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems . Journal of Computational Chamistry40 475 - 481 2019Reviewed International coauthorship
Naohiro Nishikawa, Yoshitake Sakae, Takuya Gouda, Yuichiro Tsujimura and Yuko Okamoto . Structual Analysis of a Trimer of Beta2-Microgloblin Fragment by Molecular Dynamics Simulations . Biophysical Journal116 781 - 790 2019Reviewed
Yukihiro Itoh, Yusuke Nakashima, Shuichiro Tsukamoto, Takashi Kurohira, Miki Suzuki, Yoshitake Sakae, Masayuki Oda, Yuko Okamoto, and Takayoshi Suzuki . N+-C-H…O Hydrogen bonds in protein-ligand complexes . Scientific Reports9 767 2019Reviewed
Shin Kawano, Yasushi Tamura, Rieko Kojima, Siqin Bala, Eri Asai, Agnès H. Michel, Benoît Kornmann, Isabelle Riezman, Howard Riezman, Yoshitake Sakae, Yuko Okamoto, Toshiya Endo . Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES . Journal of Cell Biology217 959 - 974 2018Reviewed International coauthorship
Shuichiro Tsukamoto Yoshitake Sakae, Yukihiro Itoh, Takayoshi Suzuki and Yuko Okamoto . Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations . Journal of Chemical Physics148 125102 2018Reviewed
Yoshitake Sakae, Tadashi Saitoh, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, Yuya Isoda, Shigeru Iida, Yuko Okamoto and Koichi Kato . Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcgamma receptor IIIa . Scientific Reports7 13780 2017
Ying Zhang, Takumi Yamaguchi, Tadashi Satoh, Maho Yagi-Utsumi, Yukiko Kamiya, Yoshitake Sakae, Yuko Okamoto and Koichi Kato . Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation . Advances in Experimental Medicine and Biology842 217 - 230 2015Reviewed International coauthorship
Norishiro Nishikawa, Yoshitake Sakae and Yuko Okamoto . Molecular Dynamics Simulations to Clarify the Concentration Dependency of Protein Aggregation . JPS Conference Proceedings5 011020 (7 pages) 2015Reviewed
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii and Yuko Okamoto . Conformational search simulations of Trp-cage using genetic crossover . Molecular Simulation41 1045 - 1049 2015Reviewed
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii and Yuko Okamoto . A conformational search method of protein systems using genetic crossover and metropolis criterion . Journal of Physics: Conference Series487 012003 2014Reviewed
Takumi Yamaguchi, Yoshitake Sakae Ying Zhang, Sayoko Yamamoto, Yuko Okamoto and Koichi Kato . Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation, Angewandte Chemie International Edition . Angewandte Chemie International Edition53 10941 - 10944 2014Reviewed
Yoshitake Sakae and Yuko Okamoto . Amino-acid-dependent main-chain torsion-energy terms for protein systems . Journal of Chemical Physics138 064103(8pages) 2013Reviewed
Yoshitake Sakae and Yuko Okamoto . Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion . Molecular Simulation39 83 - 93 2013Reviewed
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki and Yuko Okamoto . Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover . Journal of Computational Chemistry32 1353 - 1360 2011
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki and Yuko Okamoto . New conformational search method using genetic algorithm and knot theory for proteins . Pacific Symposium on Biocomputing 16 217 - 228 2011Reviewed
Yoshitake Sakae and Yuko Okamoto . Optimisation of OPLS-UA force-field paramters for protein systems using protein data bank . Molecular Simulation36 1148 - 1156 2010Reviewed
Yoshitake Sakae and Yuko Okamoto . Controlling the seconday-structure-forming tendencies of proteins by a backbone torsion-energy term . Molecular Simulation36 138 - 158 2010Reviewed
Yoshitake Sakae and Yuko Okamoto . Determination method of the balance of the secondary -structure-forming tendencies of force fields . Molecular Simulation36 159 - 165 2010Reviewed
Yoshitake Sakae and Yuko Okamoto . Folding simulations of three proteins having all alpha-helix, all beta-strand and alpha/beta-structures . 36 302 - 310 2010
Yoshitake Sakae, Toshiaki Matsubara, Misako Aida, Hidemasa Kondo, Kazuo Masaki and Haruyuki Iefuji . ONIOM study of the mechanism of the enzymatic hydrolysis of biodegradable plastics . Bulletin of the Chemical Society of Japan82 338 - 346 2009Reviewed
Yoshitake Sakae and Yuko Okamoto . Generalized-ensemble algorithms for protein structure predictions . Proceedings of International Conference on Computational & Experimental Engineering and Sciences 2009 (ICCES’09) 791 - 801 2009Reviewed
Yoshitake Sakae and Yuko Okamoto . Molecular simulations using a new torsion-energy term for protein systems . Proceedings of the International Symposium on Frontiers of Computational Science 2008 213 - 220 2008Reviewed
Jun Nakazawa, Yoshitake Sakae, Misako Aida and Yoshinori Naruta . Kinetic investigations of the process of encapsulation of small hydrocarbons into a cavitand-porphyrin . Journal of Organic Chemistry72 9448 - 9455 2007Reviewed
Yoshitake Sakae and Yuko Okamoto . Secondary-structure design of proteins by a backbone torsion energy . Journal of the Physical Society of Japan75 054802(9pages) 2006Reviewed
Yoshitake Sakae and Yuko Okamoto . Protein force-filed parameters optimized with the Protein Data Bank. II. Comparisons of force fields by folding simulations of short peptides . Journal of Theoretical and Computational Chemistry3 359 - 378 2004Reviewed
Yoshitake Sakae and Yuko Okamoto . Protein force-filed parameters optimized with the Protein Data Bank. I. Force-field optimizations . Journal of Theoretical and Computational Chemistry3 339 - 358 2004Reviewed
Yoshitake Sakae and Yuko Okamoto . Optimization of protein force-field parameters with the Protein Data Bank . Chemical Physics Letters382 626 - 636 2003Reviewed
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes Reviewed
Yoshitake Sakae, Yuko Okamoto（ Role： Joint author , Optimizations of Protein Force Fields）
Springer Cham 2014 （ ISBN:978-3-319-95843-9 ）
分子動力学シミュレーションによる医学・創薬に向けたタンパク質の構造解析 Reviewed
榮 慶丈、西川 直宏、塚本 修一朗、鈴木 孝禎、岡本 祐幸（ Role： Joint author）
薬学雑誌 136 巻 2016
A Mini-review on Chemoinfomatics Approaches for Drug Discovery Reviewed
Norihito Kawashita, Hiroyuki Yamasaki, Tomoyuki Miyao, Kentato Kawai, Yoshitake Sakae, Takeshi Ishikawa, Kenichi Mori, Shinya Nakamura, Hiromasa Kaneko（ Role： Joint author）
Journal of Computer Aided Chemistry 16 2015
タンパク質系分子シミュレーションのための力場関数 Reviewed
榮 慶丈、依田 隆夫、杉田 有治、岡本 祐幸（ Role： Joint author）
日本物理学会会誌 67 巻 2012
タンパク質系のポテンシャル関数の比較と改良 Reviewed
榮 慶丈、依田 隆夫、杉田 有治、岡本 祐幸（ Role： Joint author）
分子シミュレーション研究会会誌 “アンサンブル”, VOL. 11 2009
PDBデータベースを用いたタンパク質力場パラメータの最適化 Reviewed
榮 慶丈、岡本 祐幸（ Role： Joint author）
生物物理 VOL. 45 2005
PDBデータベースによる力場パラメータの最適化 Reviewed International journal
榮 慶丈、岡本 祐幸（ Role： Joint author）
分子シミュレーション研究会会誌 “アンサンブル” VOL. 6 2004
Ito Shota, Tsujikawa Koyo, Sahashi Kentaro, Kawasaki Takeshi, Sakae Yoshitake, Katsuno Masahisa 分子動力学シミュレーションとアンブレラサンプリングによる神経疾患関連フィラミンA変異の構造解析(Molecular Dynamics and Umbrella Sampling Reveal Structural Changes in Filamin-A Mutants associated with Neurodegenerative disorders)
生物物理 2025.8 (一社)日本生物物理学会
榮 慶丈 分子シミュレーションで用いるタンパク質系力場の改良 Invited
第 10 回日本蛋白質科学会年会 2010.6
榮 慶丈 拡張アンサンブル法による生体分子の高次構造と機能の解明 Invited
物性研・CMSI・次世代ナノ情報合同研究会 2011.1
榮 慶丈 レプリカ交換法によるタンパク質の立体構造予測 Invited
平成 24 年度「京」を中核とする HPCI システム利用研究課題中間報告会 2013.3
Yoshitake Sakae Refinement of force-field parameters for protein systems Invited
Workshop on Molecular Simulations of Biophysics and Biochemistry 2013.11
榮 慶丈 分子動力学シミュレーションによる医学・創薬に向けたタンパク質の構造解析 Invited
日本薬学会第135年会 2015.3
Yoshitake Sakae Force fields and conformational search methods for protein system Invited International conference
Research seminar 2014.12
Yoshitake Sakae A Conformational Search Method of Molecular Simulation Using Genetic Algorithm for Protein Systems Invited International conference
The 4th IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2015.8
論文賞
2016.9 Journal of Computer Aided Chemistry A Mini-review on Chemoinfomatics Approaches for Drug Discovery
Norihito Kawashita, Hiroyuki Yamasaki, Tomoyuki Miyao, Kentato Kawai, Yoshitake Sakae, Takeshi Ishikawa, Kenichi Mori, Shinya Nakamura, Hiromasa Kaneko
Grant number：hp150134 2015.4 - 2016.3
革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI) 革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI)
榮 慶丈
Authorship：Principal investigator
Grant number：hp130108 2014.4 - 2015.3
革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI) 革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI)
榮 慶丈
Authorship：Principal investigator
Grant number：19750126 2007.4 - 2009.3
日本学術振興会 科学研究費補助金 若手研究（B）
榮 慶丈
Grant type：Competitive
Grant amount：\3190000
Grant number：18650234 2006.4 - 2007.3
日本学術振興会 科学研究費補助金 萌芽研究
原田 隆範、相田 美砂子、榮 慶丈、合田 祥子
Grant type：Competitive
Grant amount：\3300000
物理学セミナーIV-1
Level：Postgraduate Country：Japan
計算機活用演習
Level：Graduate (liberal arts) Country：Japan
自然科学研究機構など、糖鎖による抗体ダイナミクスの制御機構を解明 〜分子経絡が抗体医薬設計の新たな鍵に〜 Internet
日経BP 日経バイオテク https://bio.nikkeibp.co.jp/atcl/release/25/08/06/25188/ 2025.8
