GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Author:

Jung Jaewoon1,Mori Takaharu2,Kobayashi Chigusa1,Matsunaga Yasuhiro1,Yoda Takao3,Feig Michael4,Sugita Yuji1256

Affiliation:

1. Computational Biophysics Research Team; RIKEN Advanced Institute for Computational Science; Kobe Japan

2. Theoretical Molecular Science Laboratory; RIKEN; Wako-shi Japan

3. Nagahama Institute of Bio-Science and Technology; Nagahama Japan

4. Department of Biochemistry and Molecular Biology, and Department of Chemistry; Michigan State University; East Lansing MI USA

5. Interdisciplinary Theoretical Science Research Group; RIKEN; Wako-shi Japan

6. Laboratory for Biomolecular Function Simulation; RIKEN Quantitative Biology Center; Kobe Japan

Funder

Grant-in-Aid for Scientific Research on Innovative Areas, MEXT, Japan

Publisher

Wiley

Subject

Materials Chemistry,Computational Mathematics,Physical and Theoretical Chemistry,Computer Science Applications,Biochemistry

Reference104 articles.

1. http://www.riken.jp/TMS2012/cbp/en/research/software/genesis/index.html http://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html

2. Dynamics of folded proteins;McCammon;Nature,1977

3. Accurate simulation of protein dynamics in solution;Levitt;Proc Natl Acad Sci USA,1988

4. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution;Duan;Science,1998

5. Energetics of ion conduction through the K+ channel;Berneche;Nature,2001

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