Publications

 

Residue-residue interactions regulating the Ca2+-induced EF-hand conformation changes in calmodulin.
Hiromitsu Shimoyama and Mayuko Takeda-Shitaka.
J Biochem., doi: 10.1093/jb/mvx025 [Epub ahead of print] (2017).

Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.
Hiroyuki Nojima, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Gaku Inoue, Koichiro Atsuda, Chihiro Itoh, Chie Iguchi and Hajime Matsubara.
BMC Struct. Biol., 16:11 (2016).

CAB-align: a flexible protein structure alignment method based on the residue-residue contact area.
Genki Terashi and Mayuko Takeda-Shitaka.
PLoS One, 10, e0141440 (2015).
[Download CAB-align]

Molecular recognition study on the binding of calcium to calbindin D9k based on 3D reference interaction site model theory.
Yasuomi Kiyota and Mayuko Takeda-Shitaka.
J. Phys. Chem. B, 118, 11496-11503 (2014).

Quality assessment methods for 3D protein structure models based on a residue-residue distance matrix prediction.
Genki Terashi, Yuuki Nakamura, Hiromitsu Shimoyama and Mayuko Takeda-Shitaka.
Chem. Pharm. Bull., 62, 744-753 (2014).

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.
Proteins, 81, 1980-1987 (2013).

United3D: a protein model quality assessment program that uses two consensus based methods.
Genki Terashi, Makoto Oosawa, Yuuki Nakamura, Kazuhiko Kanou and Mayuko Takeda-Shitaka.
Chem. Pharm. Bull., 60, 1359-1365 (2012).

LB3D: a protein 3D structure search program based on the lower bound of a root mean square deviation value.
Genki Terashi, Tetsuo Shibuya and Mayuko Takeda-Shitaka.
J. Comput. Biol., 19, 493-503 (2012).

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C. Mitchell, Omar N.A Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Şefik Kerem Ovalı, Pemra Ozbek, Nir Ben Tal, Türkan Haliloglu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Pérez-Cano, Carles Pons, Juan Fernández-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li , Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Patapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley,Haruki Nakamura, Kengo Kinoshita, Camden M. Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M. J.J. Bonvin, Weiyi Zhang, Carlos J. Camacho, Krishna P. Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodríguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin, and David Baker
J. Mol. Biol., 414, 289-302 (2011).

清田泰臣
「3次元 RISM 理論に基づくドラッグデザインへ向けた解析手法の開発と応用」
分子シミュレーション研究会会誌アンサンブル, 分子シミュレーション研究会, Vol.14, p.191-195 (2012).

竹田-志鷹真由子、下山紘充
「タンパク質の立体構造と創薬」
新しい薬学事典, 朝倉書店, p.31-33 (2012).

寺師玄記
「United3D: 2つのコンセンサス法によるタンパク質予測構造評価プログラム」
SAR News, 日本薬学会構造活性相関部会, No.22, p.17-21 (2012).

竹田-志鷹真由子
「計算科学によるタンパク質間相互作用予測」
SAR News, 日本薬学会構造活性相関部会, No.18, p.2-6 (2010).