Y
Yuri Matsuzaki
Researcher at Tokyo Institute of Technology
Publications - 27
Citations - 1305
Yuri Matsuzaki is an academic researcher from Tokyo Institute of Technology. The author has contributed to research in topics: Docking (molecular) & Protein–protein interaction prediction. The author has an hindex of 11, co-authored 26 publications receiving 1248 citations. Previous affiliations of Yuri Matsuzaki include Keio University.
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Journal ArticleDOI
E-CELL: software environment for whole-cell simulation.
Masaru Tomita,Kenta Hashimoto,Koichi Takahashi,Thomas S. Shimizu,Yuri Matsuzaki,Fumihiko Miyoshi,Kanako Saito,Sakura Tanida,Katsuyuki Yugi,J. C. Venter,Clyde A. Hutchison +10 more
TL;DR: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed and a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis is constructed.
Journal ArticleDOI
Community-wide assessment of protein-interface modeling suggests improvements to design methodology
Sarel J. Fleishman,Sarel J. Fleishman,Timothy A. Whitehead,Eva-Maria Strauch,Jacob E. Corn,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,Junsu Ko,Hasup Lee,Chaok Seok,Thomas Bourquard,Julie Bernauer,Anne Poupon,Jérôme Azé,Seren Soner,Şefik Kerem Ovali,Pemra Ozbek,Nir Ben Tal,Turkan 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 Potapov,Mati Cohen,Gideon Schreiber,Yuko Tsuchiya,Eiji Kanamori,Daron M. Standley,Haruki Nakamura,Kengo Kinoshita,C.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 Praneeth 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,Joël Janin,David Baker +97 more
TL;DR: A number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments are generated, suggesting that there may be important physical chemistry missing in the energy calculations.
Journal ArticleDOI
MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data
TL;DR: The development of the protein-protein docking software package MEGADOCK, which is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy, is described.
Journal ArticleDOI
E-CELL: Software Environment for Whole Cell Simulation
Masaru Tomita,Kenta Hashimoto,Koichi Takahashi,Thomas S. Shimizu,Yuri Matsuzaki,Fumihiko Miyoshi,Kanako Saito,Sakura Tanida,Katsuyuki Yugi,J. C. Venter,Clyde A. Hutchison +10 more
TL;DR: E-CELL, a generic computer software environment for modeling a cell and conducting experiments in silico, is presented and a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis is constructed.
Journal ArticleDOI
The E-CELL project: Towards integrative simulation of cellular processes
Masaru Tomita,Kenta Hashimoto,Koichi Takahashi,Yuri Matsuzaki,Ryo Matsushima,Kanako Saito,Katsuyuki Yugi,Fumihiko Miyoshi,Hisako Nakano,Sakura Tanida,Yusuke Saito,Akiko Kawase,Naoko Watanabe,Thomas S. Simizu,Thomas S. Simizu,Yoichi Nakayama +15 more
TL;DR: Using the E-CELL system, a virtual cell with 127 genes sufficient for “self-support” is successfully constructed, which was selected from the genome of Mycoplasma genitalium the organism having the smallest known genome.