A collaborative research achievement by Senior Research Scientist Kiyoshi Yagi and colleagues has been published in Nature Communications.
2021/11/02
The online workshop Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems will be held on November 18–19. For details and registration, click here.
2021/10/06
GENESIS 1.7.0 has been released! For details, click here.
2021/09/28
A research achievement on the molecular mechanism of calcium ion transport, by Technical Staff Chigusa Kobayashi and colleagues, has been published in PNAS. Press release available.
2021/09/01
Special Postdoctoral Researcher Haeri Im has joined our team.
2021/08/01
GENESIS 2.0beta3 and 1.6.1 have been released! For details, click here.
2021/07/23
A research achievement on anharmonic vibrational analysis, by Senior Research Scientist Kiyoshi Yagi and colleagues, has been published in Journal of Chemical Theory and Computation.
2021/07/17
A research achievement on optimization of molecular dynamics simulation methods, by Senior Technical Scientist Jaewoon Jung and colleagues, has been published in Journal of Chemical Theory and Computation.
2021/07/09
Press release issued for the Nature Communications paper on ligand-binding simulations in crowded environments. For details, click here.
2021/07/09
Press release issued for research on the binding process between enzymes and their inhibitors in molecularly crowded environments. For details, click here.
2021/07/01
Special Postdoctoral Researcher Yaokun Lei has joined our team.
2021/07/01
Special Postdoctoral Researcher Yosuke Sumiya has moved to a new position.
2021/06/18
A research achievement on cryo-EM structure fitting, by Senior Research Scientist Takaharu Mori and colleagues, has been accepted in Journal of Chemical Information and Modeling.
2021/06/15
A research achievement on kinase inhibition in crowded environments, by Researcher Kento Kasahara and colleagues, has been accepted in Nature Communications.
2021/06/15
A collaborative research achievement on cycloaddition enzymes, by Researcher Soo-Young Lee and colleagues, has been accepted in Angewandte Chemie International Edition.
2021/06/15
The EU-ASEAN High-Performance Computing (HPC) Virtual School 2021 will be held online from July 5–9. Chief Scientist Yuji Sugita and Technical Staff Chigusa Kobayashi will give lectures on the third day. For details, click here.
2021/06/11
Senior Research Scientist Seongho Cheng has joined our team.
2021/05/18
A review on ligand-binding free energy calculations using GENESIS has been published in Simulation (Journal of the Japan Society for Simulation Technology).
2021/04/23
A research achievement on coarse-grained models, by Researcher Ai Shinobu and colleagues, has been accepted in Journal of Chemical Information and Modeling.
2021/04/23
A research achievement on enzyme reaction pathways, by Senior Research Scientist Kiyoshi Yagi and colleagues, has been accepted in Journal of Physical Chemistry B.
2021/04/07
A research achievement on ribose-binding protein has been published in Journal of Physical Chemistry B.
A research achievement on riboswitches has been published in Frontiers in Molecular Biosciences.
2021/04/01
Trainee Masahiro Motohashi has joined our laboratory.
2021/03/17
A research achievement on multiscale molecular dynamics simulations of ribose-binding protein, by Special Postdoctoral Researcher Weitong Ren and colleagues, has been published in Journal of Physical Chemistry B.
2021/01/29
The GENESIS training course was held online, organized by the University of Tsukuba and co-organized by RIST. For details, click here.
2021/01/21
A research achievement on the SARS-CoV-2 spike protein, by Senior Research Scientist Takaharu Mori and colleagues, has been accepted in Biophysical Journal.
2021/01/06–07
The online workshop The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations was held. For details, click here.
2020
2020/12/29
A research achievement on computational methods for protein domain motions, by Special Postdoctoral Researcher Hisham M. Dokainish and colleagues, has been published in International Journal of Molecular Sciences.
2020/12/24
GENESIS 1.6.0 has been released! For details, click here.
2020/12/21
A research achievement on molecular dynamics simulation methods, by Senior Technical Scientist Jaewoon Jung and colleagues, has been published in The Journal of Chemical Physics.
2020/11/16
A research achievement on accelerating GENESIS on the supercomputer “Fugaku,” by Senior Technical Scientist Jaewoon Jung and colleagues, has been published in Journal of Computational Chemistry.
2020/11/13
GENESIS 2.0beta has been released! For details, click here.
2020/10/28
A collaborative research paper on the CHARMM-GUI Free Energy Calculator has been published in Journal of Chemical Theory and Computation.
2020/10/26
A collaborative research paper on Atg9 has been published in Nature Structural & Molecular Biology.
Special Postdoctoral Researcher Daisuke Matsutake has moved to a new position.
2020/04/13
A collaborative research paper on intrinsically disordered proteins has been published in Nature Chemical Biology.
2020/04/01
Special Postdoctoral Researcher Mao Oide has joined our team.
2020/04/01
Dr. Yosuke Sumiya’s position has changed from Special Postdoctoral Researcher to Special Postdoctoral Researcher in Basic Science.
2020/03/31
Researcher Kento Kasahara has moved to a new position.
2020/03/23
A paper on the Heme ABC transporter has been published in Journal of Physical Chemistry Letters.
2020/01/28
A review on data assimilation has been published in Current Opinion in Structural Biology.
2019
2019/12/05
A paper by Special Postdoctoral Researcher Daisuke Matsutake and colleagues has been published in Journal of Computational Chemistry.
2019/12/04
A paper by Special Postdoctoral Researcher Donatas Surblys and colleagues has been published in Journal of Membrane Science.
2019/12/03
The results of binding free energy calculations using the gREST/REUS method have been featured in RIKEN Research Highlights. For details, click here.
2019/12/01
Special Postdoctoral Researcher Shingo Ito has joined our team.
2019/11/29
A research achievement by Special Postdoctoral Researcher Ai Shinobu and colleagues has been published in Biophysics and Physicobiology.
2019/11/25
A paper on the Implicit Micelle Model, by Senior Research Scientist Takaharu Mori and colleagues, has been published in Journal of Chemical Theory and Computation.
2019/11/01
Announcement: Workshop on Molecular Dynamics Based Binding Free Energy Calculations, Post-processing of Trajectories, and Force Field Development, November 20–22, 2019 (Warsaw, Poland). For details, click here.
A collaborative research achievement on AMPA receptors has been published in Structure.
2019/09/30
A research achievement by Researcher Taku Ojima and colleagues has been published in Journal of Chemical Theory and Computation.
2019/09/10
Announcement: Workshop on Molecular Dynamics Based Binding Free Energy Calculations, Post-processing of Trajectories, and Force Field Development, November 20–22, 2019 (Warsaw, Poland). For details, click here.
2019/09/06
Press release issued for the Proceedings of the National Academy of Sciences USA paper on binding simulations using the gREST/REUS method. For details, click here.
2019/09/01
Special Postdoctoral Researcher Yosuke Sumiya has joined our team.
2019/08/30
Announcement: The 57th Annual Meeting of the Biophysical Society of Japan, Symposium “Multifaceted Approaches Toward an Integrated Understanding of Genome Function Expression,” September 24, 2019 (Miyazaki). For details, click here.
2019/08/27
Announcement: Prof. Chen Song (Peking University), August 27, 2019 (Wako Campus).
2019/08/07
A paper by Special Postdoctoral Researcher Ai Niitsu and colleagues has been published in Journal of Chemical Information and Modeling.
2019/08/05
A research achievement by Researcher Jaewoon Jung and colleagues has been published in Journal of Computational Chemistry.
2019/07/30
A research achievement by Special Postdoctoral Researcher Koichi Tamura and colleagues has been published in Journal of Physical Chemistry B.
2019/07/12
A review on simulations in cellular environments has been published in Annual Review of Cell and Developmental Biology.
2019/07/08
Announcement: Prof. Ove Christiansen (Aarhus University), Prof. Daisuke Kihara (Purdue University), July 8, 2019 (Wako Campus).
2019/07/01
Alexander T. Hino, International Program Associate, has joined our laboratory.
2019/05/31
Announcement: Assoc. Prof. Toru Shiozaki (Northwestern University), May 31, 2019 (Wako Campus).
2019/05/30
Announcement: Dr. Arina Afanasyeva, Dr. Chieko Nagao, Dr. Kenji Mizuguchi (National Institutes of Biomedical Innovation, Health and Nutrition), May 30, 2019 (Kobe, IIB). For details, click here.
2019/05/21
Announcement: The 19th Annual Meeting of the Protein Science Society of Japan, Symposium “Computational Simulations of Protein–Protein and Protein–Nucleic Acid Interactions in Cellular Environments,” June 26, 2019 (Kobe). For details, click here.
2019/05/03
The review article on Weight Averaged Anharmonic Vibrational Calculations has been published in Molecular Spectroscopy (Chapter 5).
2019/05/01
Special Postdoctoral Researcher Cheng Tan has joined our team.
2019/04/20
RIKEN Open Day, April 20, 2019 (Sat) (Wako Campus). For details, click here.
2019/04/17
A paper on simulations of ultra-large systems (GATA4), by Senior Technical Scientist Jaewoon Jung and colleagues, has been published in Journal of Computational Chemistry.
2019/04/16
Special Postdoctoral Researcher Weitong Ren has joined our team.
2019/03/31
Special Postdoctoral Researcher Marta Kulik has moved to a new position.
2019/03/31
Researcher Kosuke Matsunaga has moved to a new position.
2019/03/11
Announcement: Prof. Wonpil Im (Lehigh University), March 11, 2019 (Wako Campus).
2019/03/07
Announcement: Prof. Kenneth M. Merz, Jr. (Michigan State University), March 7, 2019 (Wako Campus).
2019/02/15
A research achievement by Researcher Taku Ojima and colleagues has been published in Biophysical Journal.
2019/02/07
A paper on anharmonic vibrational analysis using hybrid QM/MM calculations has been published in Journal of Chemical Theory and Computation.
2019/01/31
Special Postdoctoral Researcher Bo Thomsen has moved to a new position.
2018
2018/12/28
George A. Pantelopulos, International Program Associate, has returned to his home country.
2018/12/05
Announcement: Prof. Daniel M. Zuckerman (Oregon Health & Science University), December 5, 2018 (Wako Campus).
2018/11/30
Special Postdoctoral Researcher Kenta Yamada has moved to a new position.
2018/11/23
A paper on optimal temperature evaluation enabling the use of large time steps has been published in Journal of Chemical Theory and Computation.
2018/11/12
Announcement: Prof. John E. Straub (Boston University), Assoc. Prof. Naoyuki Miyashita (Kindai University), and Prof. Hiroyuki Okamoto (Nagoya University), November 12, 2018 (Wako Campus).
2018/10/26
Announcement: Dr. Robert Best (NIH), October 26, 2018 (Wako Campus).
2018/10/18
A paper on accelerating cryo-EM fitting has been published in Structure.
2018/09/20
A research achievement by Special Postdoctoral Researcher Marta Kulik and colleagues has been published in Nucleic Acids Research.
2018/09/01
Special Postdoctoral Researcher Ai Shinobu has joined our team.
2018/08/06
Announcement: Prof. Heather Kulik (Massachusetts Institute of Technology), August 6, 2018 (Wako Campus).
2018/07/02
George A. Pantelopulos, International Program Associate, has joined our laboratory.
2018/06/29
Announcement: Prof. Patrick Barth (Baylor College of Medicine), June 29, 2018 (Wako Campus).
2018/06/27
Researcher Takaharu Mori received both the “Young Scientist Award” and the “Young Scientist Award for Excellence” at the 18th Annual Meeting of the Protein Science Society of Japan.
2018/06/18
GENESIS 1.3.0, in which gREST is implemented, has just been released! More
2018/05/07
A paper on the generalized REST (gREST) method has been published in The Journal of Chemical Physics.
2018/05/03
A paper on data assimilation for Markov State Models has been published in eLife.
2018/04/30
A paper on revising Markov State Models using machine learning has been published in The Journal of Chemical Physics.
2018/04/26
A paper on multiple time step (MTS) integration has been published in The Journal of Chemical Physics.
2018/04/26
A paper on the structure of APP C99 has been published in Biochimica et Biophysica Acta.
2018/04/02
RIKEN Open Day, April 21, 2018 (Sat) (Wako Campus). For details, click here.
2018/04/02
Researcher Kento Kasahara has joined our team.
2018/04/02
Special Postdoctoral Researcher Hisham Dokainish has joined our team.
2018/04/02
Special Postdoctoral Researcher Motoji Kamiya has moved to a new position.
2018/03/30
Researcher Yuseok Yu and Special Postdoctoral Researcher Donatas Surblys have moved to new positions. Trainee Takuya Yuasa has graduated.
2018/03/09
Announcement: Mr. Tomasz Pieńko and Prof. Joanna Trylska (University of Warsaw), March 9, 2018 (Wako Campus).
2018/03/06
A research achievement by Researcher Kosuke Matsunaga and colleagues has been published in eLife.
2018/02/28
Announcement: Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory), February 28, 2018 (Wako Campus).
2018/02/07
A research achievement by Senior Research Scientist Kiyoshi Yagi and colleagues has been published in Physical Chemistry Chemical Physics.
2018/01/26
A paper on the structure of N-glycans has been published in Scientific Reports.
2017
2017/12/31
Special Postdoctoral Researcher Po-Hung Wang has moved to a new position. Intern George A. Pantelopulos has returned to his home country.
2017/12/25
Announcement: Dr. Tomotaka Origuchi (Keio University), December 25, 2017 (Wako Campus).
2017/11/29
Announcement: Prof. Kenneth M. Merz Jr. (Michigan State University), November 29, 2017 (Wako Campus).
2017/11/20
A paper discussing protein diffusion in molecularly crowded environments has been published in Journal of Physical Chemistry B.
2017/11/09
Announcement: Prof. Huan-Xiang Zhou (University of Chicago, Illinois), November 9, 2017 (Kobe, IIB). For details, click here.
2017/10/26
Announcement: Assoc. Prof. Shigeki Kiyonaka and Prof. Tadashi Hamachi (Kyoto University), October 26, 2017 (Kobe, IIB). For details, click here.
2017/09/21
Special Postdoctoral Researcher Ai Niitsu received the “Young Scientist Award” at the 55th Annual Meeting of the Biophysical Society of Japan. For details, click here.
2017/09/15
Prof. Huan-Xiang Zhou (University of Illinois at Chicago) has joined our laboratory as a sabbatical visitor (stayed until November 5).
2017/08/31
A review on intracellular molecular dynamics has been published in Molecular Science (Journal of the Molecular Science Society of Japan).
2017/08/03
A paper on the development of GENESIS 1.1 by Researchers Chigusa Kobayashi, Jaewoon Jung, and colleagues has been published in Journal of Computational Chemistry.
2017/08/01
Intern George A. Pantelopulos (JSPS Fellow) has joined our laboratory.
2017/07/29
A review on membrane protein simulations has been published in Igaku no Ayumi.
2017/07/19
A collaborative research achievement with the Shiro Laboratory of Bioinorganic Chemistry has been published in Proceedings of the National Academy of Sciences.
2017/07/18
A paper on GENESIS 1.1 has been published in Journal of Computational Chemistry.
2017/06/30
A review on intracellular molecular dynamics has been published in Journal of Physical Chemistry B.
2017/06/21
Special Postdoctoral Researcher Ai Niitsu received both the “Young Scientist Award” and the “Young Scientist Award for Excellence” at the 17th Annual Meeting of the Protein Science Society of Japan. For details, click here.
2017/06/09
A research achievement by Special Postdoctoral Researcher Bo Thomsen and colleagues has been published in Journal of Physical Chemistry B.
2017/05/02
A collaborative research achievement with the Tsukazaki Laboratory (NAIST) has been published in Cell Reports.
2017/04/24
A research achievement by Special Postdoctoral Researcher Raimondas Galvelis and colleagues has been published in Journal of Chemical Theory and Computation.
2017/04/21
A research achievement by Senior Research Scientist Osamu Miyashita and colleagues has been published in Journal of Computational Chemistry.
2017/04/21
A research achievement by Researcher Jaewoon Jung and colleagues has been published in Journal of Computational Chemistry.
2017/04/20
Announcement: Prof. Joanna Trylska (University of Warsaw), April 20, 2017 (Wako Campus).
2017/04/11
A research achievement by Special Postdoctoral Researcher Raimondas Galvelis and colleagues has been published in Journal of Chemical Theory and Computation.
2017/04/01
Special Postdoctoral Researcher Ai Niitsu has joined our team.
2017/04/01
Special Postdoctoral Researcher Ai Niitsu has moved to a new position.
2017/03/31
Mitsuhiro Sueyasu (Research Student) and Dr. Raimondas Galvelis (Postdoctoral Researcher) moved.
2017/03/31
Trainee Masanaka Sueyasu and Special Postdoctoral Researcher Raimondas Galvelis have moved to new positions.
2017/03/09
A research achievement by Researcher Kiyoshi Yagi and colleagues has been published in Journal of Physical Chemistry A.
2017/02/27
Announcement: Frontiers in Computational Biophysics and Biochemistry, February 27 – March 1, 2017 (Kobe). For details, click here.
2017/02/02
A research achievement by Researcher Tadashi Ando (currently Tokyo University of Science) and colleagues has been published in Journal of Physical Chemistry B.
2017/01/09
A research achievement by Special Postdoctoral Researcher Po-Hung Wang and colleagues has been published in Chemical Physics Letters.
