GENESIS papers

2017

Dynamics of Nitric Oxide Controlled by Protein Complex in Bacterial System
Erina Terasaka, Kenta Yamada, Po-Hung Wang, Kanta Hosokawa, Raika Yamagiwa, Kimi Matsumoto, Shoko Ishii, Takaharu Mori, Kiyoshi Yagi, Hitomi Sawai, Hiroyuki Arai, Hiroshi Sugimoto, Yuji Sugita, Yoshitsugu Shiro, and Takehiko Tosha
Proc. Natl. Acad. Sci. USA 114, 9888 (2017).


Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF
Arata Furukawa, Kunihito Yoshikaie, Takaharu Mori, Hiroyuki Mori, Yusuke V. Morimoto, Yasunori Sugano, Shigehiro Iwaki, Tohru Minamino, Yuji Sugita, Yoshiki Tanaka, and Tomoya Tsukazaki
Cell Reports 19, 895-901 (2017).


Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics
Raimondas Galvelis, Suyong Re, and Yuji Sugita
J. Chem. Theory Comput. 13, 1934-1942 (2017).


Flexible Fitting to Cryo-EM Density Map Using Ensemble Molecular Dynamics Simulations
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, and Florence Tama
J. Comp. Chem. 38, 1447-1461 (2017).


Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding
Po-hung Wang, Isseki Yu, Michael Feig, and Yuji Sugita
Chem. Phys. Lett. 671, 63-70 (2017).


GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, and Yuji Sugita
J. Comput. Chem. 38, 2193 (2017).


Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
Jaewoon Jung and Yuji Sugita
J. Comput. Chem. 38, 1410 (2017).


2016

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, and Michael Feig
eLife 5, e19274 (2016).


Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model
Tadashi Ando, Isseki Yu, Michael Feig, and Yuji Sugita
J. Phys. Chem. B 120, 11856-11865 (2016).


Graphics processing unit acceleration and parallelization of GENESIS for large-scale molecular dynamics simulations
Jaewoon Jung, Akira Naruse, Chigusa Kobayashi, and Yuji Sugita
J. Chem. Theory Comput. 12, 4947 (2016).


Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, and Yuji Sugita
BBA-Biomembranes, 1858, 1635-1651 (2016).


Dimensionality of collective variables for describing conformational changes of a multi-domain protein
Yasuhiro Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, and Yuji Sugita
J. Phys. Chem. Lett., 7, 1446-1451 (2016).


Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
Comp. Phys. Comm., 200, 57-65 (2016).  


2015

Sequential data assimilation for single-molecule FRET photon-counting data
Yasuhiro Matsunaga, Akinori Kidera, and Yuji Sugita
J. Chem. Phys., 142, 214115 (2015).


Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins
Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, and Yuji Sugita
J. Phys. Chem. B, 119, 14584-14593 (2015).


Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound state
Yoshiki Tanaka, Yasunori Sugano, Mizuki Takemoto, Takaharu Mori, Arata Furukawa, Tsukasa Kusakizako, Kaoru Kumazaki, Ayako Kashima, Ryuichiro Ishitani, Yuji Sugita, Osamu Nureki, and Tomoya Tsukazaki
Cell Reports, 13, 1561-1568 (2015).


Replica state exchange metadynamics for improving the convergence of free energy estimates
Raimondas Galvelis and Yuji Sugita
J. Comput. Chem., 36, 1446-1455 (2015).


GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, and Yuji Sugita
WIREs Comput. Mol. Sci., 5, 310-323 (2015).  


2014

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations
Jaewoon Jung, Takaharu Mori, and Yuji Sugita
J. Comput. Chem., 35, 1064-1072 (2014).


2013

Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems
Takaharu Mori, Jaewoon Jung, and Yuji Sugita
J. Chem. Theory Comput., 9, 5629-5640 (2013).


Efficient lookup table using a linear function of inverse distance squared
Jaewoon Jung, Takaharu Mori, and Yuji Sugita
J. Comput. Chem., 34, 2412-2420 (2013).


Other publications

publication lists
  • バクテリア細胞質の全原子分子動力学計算-スーパーコンピュータ「京」で複雑な構造と運動を明らかに- 理化学研究所 (2016年11月1日)
  • 超並列分子動力学計算ソフトウェア「GENESIS」を開発-「京」を活用し巨大生体分子システムのシミュレーションを実現- 理化学研究所 (2015年5月8日) 
  • The genesis of GENESIS-RIKEN Research SUMMER 2015 
  • 「京」とGENESIS で細胞の中を観る-RIKEN NEWS 2015年10月号 
  • 「京」を活用して巨大生体分子システムの分子動力学シミュレーションを実現-BioSupercomputing Newsletter 2015年9月号 
  • 速く!大規模に!精密に!タンパク質の動きを解析する超並列分子動力学計算ソフトウェア「GENESIS」- 理化学研究所計算科学研究機構 
  • “理研、生体分子解析シミュレーションソフト「GENESIS」を無償公開” 日刊工業新聞 25面(2015年5月26日)
  • “タンパク質分析より詳細に シミュレーションソフト開発 「京」で活用 創薬への応用期待” 神戸新聞 11面 (2015年5月16日)
  • “理研、超並列分子動力学計算ソフトウェアを開発―スパコン「京」で巨大生体分子システムをシミュレーション” 財経新聞 (2015年5月12日) 
  • “理研、超並列分子動力学計算ソフト「GENESIS」を無償公開” マイナビニュース (2015年5月11日) 
  • “並列計算高速に、理研、スパコン向けソフト、新薬開発に道” 日経産業新聞10面 (2015年5月9日)
  • “理研、スパコン向けシミュレーションソフトを OSS で公開” インターネットコム (2015年5月9日) 
  • “理研、分子動力学シミュレーションソフト「GENESIS」を無償公開” PC Watch (2015年5月8日)