News2017-2021

2022

2022/09/06Publication
The paper on the optimal NBFIX scaling parameter for the CHARMM36m force field has been published in Molecules.
2022/04/08Announce
Dr. Yuji Sugita received “the Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology (Awards for Science and Technology, Research Category)”.
2022/04/02Publication
The paper on the efficient algorithm for the free-energy perturbation has been accepted in J. Chem. Inf. Model.
2022/03/31Publication
The paper on the protocols for sampling of ligand binding pathways using 2-dimensional REMD has been accepted in Front. Mol. Biosci.
2022/03/23Announce
We received “FY2021 RIKEN EIHO Award (RIKEN Significant Achievement Award)”.

2021

2021/11/02Announce
Online workshop “Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems” will be held (18-19 Nov) More
2021/10/06Announce
GENESIS 1.7.0 has been released! More
2021/07/15Publication
The paper on MD simulations with a large time step using HMR and accurate T/P evaluation has been accepted in J. Chem. Theory Comput.
2021/07/09Publication
The paper on the ligand binding mechanism in crowded protein solution (Nat. Comm.) has been press released. More
2021/06/15Publication
The paper on the ligand binding mechanism in crowded protein solution has been accepted in Nat. Comm.
The paper on the molecular basis for Diels-Alderases has been accepted in Angew. Chem. Int. Ed.
2021/06/11People
Dr. Song-Ho Chong (Senior Scientist) has joined to our group.
2021/05/21Publication
The paper on Multi-basin Go̅ model has been accepted in J. Chem. Inf. Model.
2021/05/18Publication
The review paper on ligand binding free energy calculation has been published in Simulation (Journal of Japan Society for Simulataion Technology) (in Japanese).
2021/04/07Publication
The paper on ribose binding protein has been published in J. Phys. Chem. B.
The paper on riboswitch has been published in Front. Mol. Biosci.
2021/01/21Publication
The paper on SARS-CoV-2 Spike Protein has been accepted in Biophys. J.

2020

2020/12/17Announce
Workshop Announcement : The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations, Jan. 6-7, 2021 (Online) More
2020/09/03Announce
GENESIS 1.5.1 has been released. More
2020/09/01People
Dr. Daiki Matsubara (Research Scientist) has joined to our group.
2020/07/01People
Dr. Ai Shinobu (Research Scientist) has joined to our group.
2020/06/01People
Dr. Suyong Re moved.
2020/05/01Announce
GENESIS 1.5.0 has been released. More
2020/04/01People
Dr. Kento Kasahara moved.

2019

2019/12/03Publication
The work on gREST/REUS binding simulation was introduced in RIKEN research highlights. More
2019/10/31Announce
GENESIS 1.4.0 has been released. More
2019/10/05Publication
The paper on the AMPA receptor has been published in Structure.
2019/09/30Publication
The paper by Dr. Hiraku Oshima et al. has been published in J. Chem. Theory Comput.
2019/09/10Announce
Workshop Announcement : Workshop on molecular dynamics based binding free energy calculations, post-processing of trajectories and force field development, Nov. 20-22, 2019 (Warsaw, Poland)More
2019/09/06Publication
The paper on gREST/REUS binding simulation (Proc. Natl. Acad. Sci. USA) has been press released. More
2019/08/26Publication
The paper by Dr. Suyong Re et al. has been published in Proc. Natl. Acad. Sci. USA.
2019/08/09Publication
The review article on the replica-exchange molecular dynamics has been published in Methods in molecular biology.
2019/08/07Publication
The paper by Dr. Ai Niitsu et al. has been published in J. Chem. Inf. Model.
2019/05/30Announce
Seminar Announcement : Dr. Arina Afanasyeva, Dr. Chioko Nagao, Dr. Kenji Mizuguchi (NIBIOHN) May 30th, 2019 (Kobe, IIB)More
2019/05/07Publication
The review article on the glycan simulation has been accepted by Trends Glycosci. Glycotechnol.
2019/02/15Publication
The paper by Dr. Hiraku Oshima et al. has been published in Biophys. J.

2018

2018/04/02People
Dr. Kento Kasahara (Postdoctoral Researcher) has joined to our group.
2018/01/26Publication
The paper by Dr. Suyong Re et al. has been published in Sci. Rep..

2017

2017/10/26Announce
Seminar Announcement : Prof. Shigeki Kiyonaka, Prof. Itaru Hamachi (Kyoto University) Oct. 26th, 2017 (Kobe, IIB) More
2017/08/03Paper
The paper on GENESIS1.1 has been published in J. Comput. Chem.
2017/06/30Paper
The paper on the MD simulations of crowding in cellular environments has been published in J. Phys. Chem. B
2017/04/21Paper
The paper on the RSE-MTD method has been published in J. Chem. Theory Comput.
2017/04/01People
Dr. Ai Niitsu moved.
2017/02/02Paper
The paper by Dr. Tadashi Ando has been published in J. Phys. Chem. B.