News2017-2021

2021

2021/11/11Publication
A collaborative research work by Dr. Kiyoshi Yagi et al. has been published in Nat. Commun..
2021/11/02Announce
We are co-hosting an online workshop “Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems” (18-19 Nov). Click here for details and registration
2021/10/06Announce
GENESIS 1.7.0 has been released! Click here for details
2021/09/28Publication
A research paper about molecular mechanism of Calcium ion transport by Dr. Chigusa Kobayashi et al. has been published in PNAS. Press Release (J)
2021/09/01People
Dr. Haeri Im (Postdoctral Researcher) has joined our group.
2021/08/01Announce
GENESIS 2.0beta3 and 1.6.1 have been released! Click here for details
2021/07/23Publication
A research paper about development of an efficient anharmonic vibrational method by Dr. Kiyoshi Yagi et al. has been published in J. Chem. Theory Comput.
2021/07/17Publication
A research paper about optimization of MD simulation method by Dr. Jaewoon Jung et al. has been published in J. Chem. Theory Comput.
2021/07/09Announce
Press release regarding our work on Kinase inhibition in a crowded environment Click here for details
2021/07/01People
Dr. Yaokun Lei (Postdoctral Researcher) has joined our group.
2021/07/01People
Dr. Yosuke Sumiya (Special Postdoctral Researcher) has left our group.
2021/06/18Publication
A research paper about flexible fitting refinement for Cryo-EM structures by Dr. Takaharu Mori et al. has been accepted in J. Chem. Inf. Model.
2021/06/15Publication
A research paper about Kinase inhibition in crowded solution by Dr. Kento Kasahara et al. has been accepted in Nat. Commun.
2021/06/15Publication
A research paper about Diels-Alderase by Dr. Suyong Re et al. has been accepted in Angew. Chem. Int. Ed.
2021/06/15Announce
Join us at EU-ASEAN High-Performance Computing (HPC) Virtual School 2021! Dr. Sugita and Dr. Kobayashi will give a lecture on the 3rd day. Click here for details
2021/04/23Publication
A research paper about coarse-grained modeling by Dr. Ai Shinobu et al. has been accepted in J. Chem. Inf. Model.
2021/04/23Publication
A research paper about pathways of enzymatic reactions by Dr. Kiyoshi Yagi et al. has been accepted in J. Phys. Chem. B
2021/04/01People
Mr. Masahiro Motohashi (Trainee) has joined our group.
2021/03/17Publication
A research paper about multi-scale simulations of conformational dynamics of ribose-binding protein by Dr. Weitong Ren et al. has been published in J. Phys. Chem. B
2021/01/21Publication
A research paper about conformational stability and dynamics of spike protein on SARS-CoV-2 by Dr. Takaharu Mori et al. has been published in Biophys. J.

2020

2020/12/29Publication
A research paper about protein domain motions by Dr. Hisham M. Dokainish et al. has been published in Int. J. Mol. Sci.
2020/12/24Announce
GENESIS 1.6.0 has been released! Click here for details
2020/12/21Publication
A research paper by Dr. Jaewoon Jung et al. has been published in J. Chem. Phys.
2020/11/16Publication
A research paper about GENESIS optimization and parallelization on Fugaku by Dr. Jaewoon Jung et al. has been published in J. Comput. Chem.
2020/11/13Announce
GENESIS 2.0beta has been released! Click here for details
2020/10/28Publication
A research paper about CHARMM-GUI free-energy calculator in collaboration with Prof. Wonpil Im’s group (Lehigh U.) has been published in J. Chem. Theory Comp.
2020/10/26Publication
A research paper about Atg9 in collaboration with Dr. N.N.Noda (IMC) has been published in Nature Struct. Mol. Biol.
2020/09/03Announce
GENESIS 1.5.1 has been released! Click here for details
2020/07/31Publication
A research paper about protein-ligand binding using gREST+FEP has been published in J. Chem. Inf. Model.
2020/07/28Publication
A research paper about coarse-grained molecular dynamics method has been published in J. Chem. Phys.
2020/07/25Publication
A review article about molecular dynamics simulations of glycans has been published in Trends in Glycosci. Glycotech.
2020/05/01Announce
GENESIS 1.5.0 has been released! Click here for details
2020/05/01People
Dr. Daisuke Matsuoka (Postdoctoral Researcher) moved.
2020/04/13Publication
A research paper about Intrinsically disordered proteins in collaboration with Dr. M. Tanaka (RIKEN CBS) has been published in Nature Chem. Biol.
2020/04/01People
Dr. Mao Oide (Special Postdoctoral Researcher) has joined to our group.
2020/04/01People
Dr. Yosuke Sumiya has become a Special Postdoctoral Resercher.
2020/01/28Publication
A review on refining of conformational dynamics in molecular simulations has been published in Curr. Opin. Struct. Biol..

2019

2019/12/05Publication
A research paper by Dr. Daisuke Matsuoka has been published in J. Comput. Chem..
2019/12/04Publication
A research paper by Dr. Donatas Surblys has been published J. Memb. Sci..
2019/12/02People
Dr. Shingo Ito (Postdoctoral Researcher) has joined to our group.
2019/11/25Publication
A paper on Implicit Micelle Model has been published in J. Chem. Theory Comput..
2019/10/31Announce
GENESIS 1.4.0 has been released! Click here for details
2019/09/02People
Dr. Yosuke Sumiya (Postdoctoral Researcher) has joined to our group.
2019/08/30Announce
Symposium Announcement: The 57th Annual Meeting of the BSJ; “Integrative approaches towards understanding of gene expression” Sep. 24th, 2019 (Miyazaki) More
2019/08/27Seminar
Seminar Announcement: Prof. Chen Song (Peking University) Aug. 27th, 2019 (Wako)
2019/08/07Publication
A research paper by Dr. Ai Niitsu et al. has been published in J. Chem. Inf. Model..
2019/07/12Publication
A research paper on simulations in cellular environments has been published in Annu. Rev. Cell. Dev. Biol..
2019/07/08Seminar
Seminar Announcement: Prof. Ove Christiansen (Aarhus University), Prof. Daisuke Kihara (Purdue University) July 8th, 2019 (Wako)
2019/07/01People
Alexander T. Hino (International Program Associate) has joined to our group.
2019/05/31Seminar
Seminar Announcement: Prof. Toru Shiozaki (Northwestern University) May 31th, 2019 (Wako)
2019/05/21Announce
Workshop Announcement: The 19th Annual Meeting of the PSSJ; “Computer simulations of protein-protein and protein/DNA interactions in celluar environments” Jun. 26th, 2019 (Kobe) More
2019/05/03Publication
The review article on Weight Averaged Anharmonic Vibrational Calculations has been published in Molecular Spectroscopy (Chapter 5).
2019/04/20Announce
RIKEN’s Open Day events Announcement: Apr. 20th, 2018 (Wako)
2019/04/17Publication
The paper on simulations of a huge system (GATA4) has been published in J. Comput. Chem..
2019/04/16People
Dr. Weitong Ren (Postdoctoral Researcher) has joined to our group.
2019/03/31People
Dr. Marta Kulic (Postdoctoral Researcher) moved.
2019/03/11Seminar
Seminar Announcement: Prof. Wonpil Im (Lehigh University) Mar. 11th, 2019 (Wako)
2019/03/07Seminar
Seminar Announcement: Prof. Kenneth M. Merz, Jr. (Michigan State University) Mar. 7th, 2019 (Wako)
2019/02/07Publication
The paper on anharmonic vibrational analysis using hybrid QM/MM computation has been published in J. Chem. Theory Comput..
2019/01/31People
Dr. Bo Thomsen (Special Postdoctoral Researcher) moved.

2018

2018/12/28People
George A. Pantelopulos (International Program Associate) moved.
2018/12/05Seminar
Seminar Announcement: Prof. Daniel M. Zuckerman (Oregon Health & Science University) Dec. 5th, 2018 (Wako)
2018/11/30People
Dr. Kenta Yamada moved.
2018/11/23Publication
The paper on optimal temperature evaluation with a large time step has been published in J. Chem. Theory Comput..
2018/11/12Seminar
Seminar Announcement: Prof. John E. Straub (Boston University), Prof. Naoyuki Miyashita (Kindai University), Prof. Yuko Okamato (Nagoya University) Nov. 12th, 2018 (Wako)
2018/10/26Seminar
Seminar Announcement: Dr. Robert Best (NIH) Oct. 26th, 2018 (Wako)
2018/10/18Publication
The paper on Acceleration of Cryo-EM Flexible Fitting has been published in structure.
2018/09/20Publication
The paper by Dr. Marta Kulik et al. has been published in Nucleic Acids Research.
2018/08/06Seminar
Seminar Announcement: Prof. Heather Kulik (Massachusetts Institute of Technology) Aug. 6th, 2018 (Wako)
2018/07/02People
George A. Pantelopulos (International Program Associate) has joined to our group.
2018/06/29Seminar
Seminar Announcement: Prof. Patrick Barth (Baylor College of Medicine) Jun. 29th, 2018 (Wako)
2018/06/27Award
Dr. Takaharu Mori won “Young Scientist Excellence Award” in the 18th Annual Meeting of the Protein Science Society of Japan!
2018/06/18Announce
GENESIS 1.3.0, in which gREST is implementated, has just been released! More
2018/05/07Publication
The paper on generalized REST (gREST) has been published in J. Chem. Phys..
2018/05/03Publication
The paper on data-assimilation of Markov state model has been published in eLife.
2018/04/30Publication
The paper on refinement of Markov state models using machine learning has been published in J. Chem. Phys..
2018/04/26Publication
The paper on a multiple time step (MTS) integration has been published in J. Chem. Phys..
2018/04/24Publication
The paper on structure of APP C99 has been published in Biochim. Biophys. Acta.
2018/04/02Announce
RIKEN’s Open Day events Announcement :　Apr. 21rd, 2018 (Wako) More
2018/04/02People
Dr. Hisham Dokainish (Postdoctoral Researcher) has joined to our group.
2018/03/30People
Dr. Isseki Yu, Dr. Donatas Surblys and Takuya Yuasa moved.
2018/03/09Seminar
Seminar Announcement: Mr. Tomasz Pieńko and Prof. Joanna Trylska (University of Warsaw) Mar. 9th, 2018 (Wako)
2018/02/28Seminar
Seminar Announcement: Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory) Feb. 28th, 2018 (Wako)
2018/02/07Publication
The paper by Dr. Kiyosi Yagi et al. has been published in Phys. Chem. Chem. Phys..
2018/01/26Publication
The paper on conformation of N-glycans has been published in Scientific Reports.

2017

2017/12/31People
Dr. Po-Hung Wang (Postdoctoral Researcher) and George A. Pantelopulos (NFS GROW fellow) moved.
2017/12/25Seminar
Seminar Announcement: Dr. Tomotaka Oroguchi (Keio University) Dec. 25th, 2017 (Wako)
2017/11/29Seminar
Seminar Announcement: Prof. Kenneth M. Merz Jr (Michigan State University) Nov. 29th, 2017 (Wako)
2017/11/20Publication
The paper on protein diffusion in crowded environment has been published in J. Phys. Chem. B.
2017/09/21Award
Dr. Ai Niitsu won “Early Career Award in Biophysics” in the 55th Annual Meeting of the Biophysical Society of Japan!
2017/09/15People
Prof. Huan-Xiang Zhou (University of Illinois at Chicago) has joined our group as a sabbatical visitor. (He stayed until 11/5)
2017/08/01People
George A. Pantelopulos (NFS GROW fellow) has joined our group.
2017/07/19Publication
The collaborative research paper with Biometal Science laboratory has been published in Proc. Natl. Acad. Sci..
2017/07/18Publication
The paper on GENESIS1.1 has been published in J. Comput. Chem..
2017/06/30Publication
The review paper about crowding in cellular environment has been published in J. Phys. Chem. B.
2017/06/21Award
Dr. Ai Niitsu won “Young Scientist Excellence Award” in the 17th Annual Meeting of the Protein Science Society of Japan!
2017/06/09Publication
The paper by Dr. Bo Thomsen et al. has been published in J. Phys. Chem. B .
2017/05/02Publication
The collaborative research paper with Tsukazaki Lab. (NAIST) has been published in Cell Rep. .
2017/04/24Publication
The paper by Dr. Raimondas Galvelis et al. has been published in J. Chem. Theory Comput. .
2017/04/20Seminar
Seminar Announcement :Prof. Joanna Trylska (Centre of New Technologies, University of Warsaw) Apr. 20th, 2017 (Wako)
2017/04/11Publication
The paper by Dr. Raimondas Galvelis et al. has been published in J. Chem. Theory Comput. .
2017/04/01People
Dr. Ai Niitsu (Special Postdoctoral Researcher) has joined to our group.
2017/03/31People
Mitsuhiro Sueyasu (Research Student) and Dr. Raimondas Galvelis (Postdoctoral Researcher) moved.
2017/3/9Publication
The paper by Dr. Kiyoshi Yagi et al. has been published in J. Phys. Chem. A .
2017/01/09Publication
The paper by Dr. Po-Hung Wang et al. has been published in Chem. Phys. Lett. .