Seminar Announcement: Prof. Chen Song (Peking University) Aug. 27th, 2019 (Wako)
The paper by Niitsu et al. has been pubulished in J. Chem. Inf. Model..
The paper on simulations in celluar environments has been pubulished in Annu. Rev. Cell. Dev. Biol..
Seminar Announcement: Prof. Ove Christiansen (Aarhus University), Prof. Daisuke Kihara (Purdue University) July 8th, 2019 (Wako)
Alexander T. Hino (International Program Associate) has joined to our group.
Seminar Announcement: Prof. Toru Shiozaki (Northwestern University) May 31th, 2019 (Wako)
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)
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The review article on Weight Averaged Anharmonic Vibrational Calculations has been pubulished in Molecular Spectroscopy (Chapter 5).
RIKEN's Open Day events Announcement: Apr. 20th, 2018 (Wako)
The paper on simulations of a huge system (GATA4) has been pubulished in J. Comput. Chem..
Dr. Weitong Ren (Postdoctoral Researcher) has joined to our group.
Dr. Marta Kulik (Postdoctoral Researcher) moved.
Seminar Announcement: Prof. Wonpil Im (Lehigh University) Mar. 11th, 2019 (Wako)
Seminar Announcement: Prof. Kenneth M. Merz, Jr. (Michigan State University) Mar. 7th, 2019 (Wako)
The paper on anharmonic vibrational analysis using hybrid QM/MM computation has been pubulished in J. Chem. Theory Comput..
Dr. Bo Thomsen (Special Postdoctoral Researcher) moved.
George A. Pantelopulos (International Program Associate) moved.
Seminar Announcement: Prof. Daniel M. Zuckerman (Oregon Health & Science University) Dec. 5th, 2018 (Wako)
Dr. Kenta Yamada (Postdoctoral Researcher) moved.
The paper on optimal temperature evaluation with a large time step has been pubulished in J. Chem. Theory Comput..
Seminar Announcement: Prof. John E. Straub (Boston University), Prof. Naoyuki Miyashita (Kindai University), Prof. Yuko Okamato (Nagoya University) Nov. 12th, 2018 (Wako)
Seminar Announcement: Dr. Robert Best (NIH) Oct. 26th, 2018 (Wako)
The paper on Acceleration of Cryo-EM Flexible Fitting has been pubulished in structure.
Seminar Announcement: IPR Seminar; "Frontier of dynamic structural biology" Sep. 26-27, 2018 (Osaka Univ.)
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The paper by Dr. Marta Kulik et al. has been published in Nucleic Acids Research.
Seminar Announcement: Prof. Heather Kulik (Massachusetts Institute of Technology) Aug. 6th, 2018 (Wako)
George A. Pantelopulos (International Program Associate) has joined to our group.
Seminar Announcement: Prof. Patrick Barth (Baylor College of Medicine) Jun. 29th, 2018 (Wako)
Dr. Takaharu Mori won “Young Scientist Excellence Award” in the 18th Annual Meeting of the Protein Science Society of Japan!
GENESIS 1.3.0, in which gREST is implementated, has just been released!
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The paper on generalized REST (gREST) has been published in J. Chem. Phys..
The paper on data-assimilation of Markov state model has been pubulished in eLife.
The paper on refinement of Markov state models using machine learning has been published in J. Chem. Phys..
The paper on a multiple time step (MTS) integration has been published in J. Chem. Phys..
The paper on structure of APP C99 has been published in Biochim. Biophys. Acta.
RIKEN's Open Day events Announcement : Apr. 21rd, 2018 (Wako)
Dr. Hisham Dokainish (Postdoctoral Researcher) has joined to our group.
Dr. Isseki Yu, Dr. Donatas Surblys and Takuya Yuasa moved.
Seminar Announcement: Mr. Tomasz Pieńko and Prof. Joanna Trylska (University of Warsaw) Mar. 9th, 2018 (Wako)
Seminar Announcement: Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory) Feb. 28th, 2018 (Wako)
The paper by Dr. Kiyosi Yagi et al. has been published in Phys. Chem. Chem. Phys..
The paper on conformation of N-glycans has been published in Scientific Reports.
Dr. Po-Hung Wang (Postdoctoral Researcher) and George A. Pantelopulos (NFS GROW fellow) moved.
Seminar Announcement: Dr. Tomotaka Oroguchi (Keio University) Dec. 25th, 2017 (Wako)
Seminar Announcement: Prof. Kenneth M. Merz Jr (Michigan State University) Nov. 29th, 2017 (Wako)
The paper on protein diffusion in crowded enviroment has been published in J. Phys. Chem. B.
Dr. Ai Niitsu won "Early Career Award in Biophysics" in the 55th Annual Meeting of the Biophysical Society of Japan!
Prof. Huan-Xiang Zhou (University of Illinois at Chicago) has joined our group as a sabbatical visitor.
(He stayed until 11/5)
George A. Pantelopulos (NFS GROW fellow) has joined our group.
The collaborative research paper with Biometal Science laboratory has been published in Proc. Natl. Acad. Sci..
The paper on GENESIS1.1 has been published in J. Comput. Chem..
The review paper about crowding in cellular environment has been published in J. Phys. Chem. B.
Dr. Ai Niitsu won “Young Scientist Excellence Award” in the 17th Annual Meeting of the Protein Science Society of Japan!
The paper by Dr. Bo Thomsen et al. has been published in J. Phys. Chem. B .
The collaborative research paper with Tsukazaki Lab. (NAIST) has been published in Cell Rep. .
The paper by Dr. Raimondas Galvelis et al. has been published in J. Chem. Theory Comput. .
Seminar Announcement :Prof. Joanna Trylska (Centre of New Technologies, University of Warsaw) Apr. 20th, 2017 (Wako)
The paper by Dr. Raimondas Galvelis et al. has been published in J. Chem. Theory Comput. .
Dr. Ai Niitsu (Special Postdoctoral Researcher) has joined to our group.
Mitsuhiro Sueyasu (Research Student) and Dr. Raimondas Galvelis (Postdoctoral Researcher) moved.
The paper by Dr. Kiyoshi Yagi et al. has been published in J. Phys. Chem. A .
The paper by Dr. Po-Hung Wang et al. has been published in Chem. Phys. Lett. .
The paper by Dr. Isseki Yu et al. has been published in eLife .
The paper by Drs. Suyong Re and Wataru Nishima has been published in J. Phys. Chem. C.
The paper on the GPU acceleration of GENESIS has been published in J. Chem. Theory Comput..
The paper by Dr. Hiroki Otaki et al. has been published in J. Phys. Chem. B.
The paper by Dr. Kiyoshi Yagi et al. has been publisehd in Biophys. J..
Ms. Masako Ishikawa has left our group.
Ms. Machiko Ishigaki (Assistant) has joined to our group.
Dr. Wataru Nishima moved to Los Alamos National Lab.
GENESIS 1.1.0 has just been released!
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GENESIS website has been renewed!
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Seminar Announcement :Prof. Xuhui Huang（The Hong Kong University of Science and Technology） Jul. 19th, 2016 (Wako)
Seminar Announcement :Luigi D'Ascenzo, Dr. Filip Leonarski, Dr. Pascal Auffinger（IBMC） Jul. 4th, 2016 (Wako)
Seminar Announcement : Prof. Michael Feig (Michigan State University) and Prof. Wonpil Im (University of Kansas) May. 17th, 2016 (Wako)
Seminar Announcement : Prof. Masayoshi Nakasako (Keio University) May. 10th, 2016 (Wako)
Seminar Announcement : Prof. Joanna Trylska (Centre of New Technologies, University of Warsaw, Poland) Apr. 12th, 2016 (Wako)
Dr. Donatas Surblys (Postdoctoral Researcher) has joined to our group.
Dr. Suyong Re moved to the RIKEN QBiC.
RIKEN's Open Day events Announcement : Apr. 23rd, 2016 (Wako)
Dr. Daisuke Matsuoka (Postdoctoral Researcher) has joined to our group.
The paper by Dr. Suyong Re et al. has been published in Biophys. J..
The paper by Dr. Kiyoshi Yagi et al. has been publisehd in Phys. Chem. Chem. Phys..
The paper on the DoME model has been published in J. Phys. Chem. B.
The paper on the data assimilation has been published in J. Chem. Phys..
Seminar Announcement : Prof. James C. Gumbart (Georgia Institute of Technology, USA) Nov. 10th, 2015 (Wako)
Dr. Bo Thomsen received a letter of appreciation from Hiroshi Matsumoto, President of RIKEN, for the Best Poster of Congress Award in the 15th ICQC.
Seminar Announcement : Prof. Naresh Patwari (Indian Institute of Technology Bombay, India) Jul. 22nd, 2015 (Wako)
Dr. Hiroki Otaki moved to the Nagasaki University.
Dr. Bo Thomsen won the best poster of the congress award in the 15th International Congress of Quantum Chemistry (ICQC).
Seminar Announcement : Prof. Sihyun Ham (Sookmyung Women's University, Korea) Jun. 30th, 2015 (Wako)
The paper on the data assimilation has been published in J. Chem. Phys.
The paper by Dr. Raimondas Galvelis et al. has been published in J. Comput. Chem.
The paper on GENESIS has been published in WIREs Comput. Mol. Sci.
The paper on GENESIS (WIREs Computational Molecular Science) has been press released.
A new version of GENESIS has been released.
The paper by Dr. Po-Hung Wang et al. has been published in J. Chem. Theory Comput.
RIKEN's Open Day events Announcement : Apr. 18th, 2015 (Wako)
Dr. Kenta Yamada (Postdoctoral Researcher) has joined to our group.
Dr. Yasuaki Komuro (JSPS Research Fellow) and Dr. Pai-Chi Li (Postdoctoral Researcher) moved.
Seminar Announcement : Dr. Steven Hayward (University of East Anglia, UK) Feb. 26th, 2015 (Wako)
The collaborative research paper with Prof. M. Feig (Michigan State University) has been published in J. Mol. Graph. Model.
Seminar Announcement : Dr. Makoto Taiji（RIKEN Quantitative Biology Center）Feb. 20th, 2015 (Wako)
The paper on a hierarchical domain-motion analysis of conformational changes has been published in Proteins: Struct. Funct. Bioinf.
Dr. Wataru Mizukami moved to the Kyushu University.
Workshop Announcement : "Workshop on Frontier of Biomolecular Quantum Chemistry" Jan. 22-23, 2015 (Wako) (Official Site)
The paper by Dr. S. Re et al. has been published in J. Phys. Chem. Lett.
The paper on replica exchange MD interface (REIN) has been published in Int. J. Quantum Chem.
The paper by Mr. Y. Komuro et al. has been published in J. Chem. Theory Comput.
Workshop Announcement : "Workshop on Computer Modeling and Simulation of Biomolecular Systems" Sep. 22st, 2014 (Wako) (Official Site)
Mr. Y. Komuro won the poster presentation award in the 14th Annual Meeting of the Protein Science Society of Japan.
The collaborative research paper with Prof. O. Nureki (University of Tokyo) has been published in Nature.
The paper on the hybrid parallelization of MD simulations has been published in J. Comput. Chem.
Mr. Bo Thomsen (Technical Staff) has joined to our group.
Dr. W. Mizukami (Special Postdoctoral Researcher) and Dr. R. Galvelis (Postdoctoral Researcher) have joined to our group.
Mr. S. Watabe (Student Trainee) graduated.
Our new MD software GENESIS has been released under GPLv2 license.
Seminar Announcement : Prof. John E. Straub (Boston University, USA), Prof. Wonpil Im (The University of Kansas, USA) Mar. 6th, 2014 (Wako)
Mr. Y. Komuro won the student presentation award in 3rd international conference on molecular simulation (icsm2013).
Seminar Announcement : Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory, USA) Dec. 11th, 2013 (Wako)
The paper on the surface-tension replica-exchange molecular dynamics method has been published in J. Chem. Theory Comput.
The paper on the structure prediction of transmembrane helix dimers has been published in J. Comput. Chem.
The collaborative research paper with Dr. Takao Yoda (Nagahama Institute of Bio-Science and Technology) has been published in PROTEINS: Struct. Funct. Bioinfo.
The paper on the modeling for crowded cellular environment has been published in J. Mol. Graph. Model.
Workshop Announcement : "Molecular Simulations of Biophysics and Biochemistry" Nov. 21st, 2013 (Kobe) (Official Site)
Workshop Announcement : "Modeling Biomolecular Systems in Cellular Environment" Oct. 31st-Nov. 1st, 2013 (Kyoto) (Official Site)
Seminar Announcement : Prof. Kenneth M. Merz Jr. (Michigan State University, USA) Sept. 26th, 2013 (Wako)
The paper on the lookup table for the fast pairwise nonbonded calculations has been published in J. Comput. Chem..
The collaborative research paper with Prof. O. Nureki and R. Ishitani (University of Tokyo) has been published in Proc. Natl. Acad. Sci. USA.
Workshop Announcement : 51st Annual Meeting of the Biophysical Society of Japan "Functional dynamics of Nucleosome and Chromathin in Nuclear Crowding Environment" Oct. 29th, 2013 (Kyoto)
The collaborative research paper with Prof. C. H. Choi (Kyungpook National University, Korea) has been published in J. Phys. Chem. B.
Dr. Po-Hung Wang (Contract Researcher) have joined to our group.
Dr. Andrei Pisliakov moved to the University of Dundee, Scotland.
Workshop Announcement : 13th annual meeting of the protein science society of Japan "Computational protein science in ExaFlops era" Jun 12th, 2013 (Tottori)
Mr. Y. Komuro has been selected for the participant of 2013 International HPC Summer School.
RIKEN's Open Day events Announcement : Apr. 20th, 2013 (Wako)
Dr. T. Mori (Research Scientist), Dr. H. Otaki (Postdoctoral Fellows for Basic Science), Dr. I. Yu (Contract Researcher) have joined to our group.
Dr. C. Kobayashi (Contract Researcher) and Dr. F. Ogushi (Contract Researcher) moved to Kobe institute and Ochanomizu University, respectively.
The paper by Mr. Y. Komuro et al. has been published in J. Phys. Chem. B.
Mr. Y. Komuro has been selected for the participant of 5th HOPE MEETING.
Workshop Announcement : RIKEN symposium "Theoretical and experimental glycobiology" Mar. 12th, 2013 (Wako)
The paper on the protein stability in crowded cellular environment has been published in J. Am. Chem. Soc.
The paper on the QM/MM reaction path optimization has been published in J. Chem. Phys..
Dr. W. Mizukami (University of Bristol, UK) gave a seminar in Wako.
The collaborative research paper with Prof. C. H. Choi (Kyungpook National University, Korea) has been published in J. Phys. Chem. B.
Dr. K. Yagi (Research Scientist) has joined to our group.
Dr. K. Sanbonmatsu (Los Alamos National Laboratory, USA) gave a seminar in Wako.
A new homepage of Theoretical Molecular Science Laboratory has been opened.
"Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography." has been published in Rapid Commun. Mass Spectrom.
Dr. Sugita organizes a symposium at the 50th Annual Meeting of the Biophysical Society of Japan.
"Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules" has been published in Curr. Phys. Chem.
"Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase" has been published in PLoS Comp. Biol.
"Conformational flexibility of N-glycans in solution studied by REMD simulations" has been published in Biophys. Rev.
"Structural insights into electron transfer in caa3-type cytochrome oxidase" has been published in Nature.
"Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water" has been published in Chem. Phys. Lett.
"Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution" has been published in J. Phys. Chem. B
Ms. Yamaji (secretary) moved to Nishina center.
Dr. Sugita was promoted to a Chief Scientist and the laboratory name has been changed to Theoretical Molecular Science Laboratory.
"Crystal structure of alpha 5 beta 1 integrin ectodomain: Atomic details of the fibronectin receptor" has been published in J. Cell. Biol.
"The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation" has been published in J. Virology.
Dr. Karl N. Kirschner（SCAI、Germany）gave a seminar in Wako.
Prof. Sihyun Ham（Sookmyung Women's University, Korea）gave a seminar in Wako.
The paper on Volonoi analysis of lipid surface area in protein-membrane systems has been published in J. Comp. Chem.
The paper on flip-flop motions of lipid molecules has been published in Chem. Phys. Lett.
The paper on protein-protein interactions under the crowding environment has been published in J. Phys. Chem. B.
The paper on quinol-dependent nitric oxide reductase has been published in Nature Struct. Mol. Biol.
The paper on structural diversity of N-glycans in solution has been published in Biophysical Journal (Letter).
The paper on structural of MgFx compound in solution has been published in J. Phys. Chem. B.
The paper on drug efflux mechanism of multidrug transporter, ACRB has been published in J. Phys. Chem. B (selected as the cover of the issue).
Ms. Kayo Yamaji (Assistant) have joined in our group.
Ms. Wakayo Taira (Assistant) have joined in our group.
Dr. Chigusa Kobayashi (Contract Researcher) and Dr. Wataru Nishima (Postdoctral Researcher) have joined in our group.
Dr. Takashi Imai (Senior Scientist) and Dr. Naoyuki Miyashita (Research Scientist) moved to the Laboratory for Biomolecular Function Simulation in Quantitative Biology Center (QBiC, Kobe).
Laboratory for Biomolecular Function Simulation (Team Leader Yuji Sugita /Additional Post), Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC) officially opened.
Ms. Mai Usui (Assistant) resigned from our group.
Position opend for the Foreign Postdoctoral Researcher (FPR) program in RIKEN (Deadline: 2011/5/20）
Prof. Michael Feig (Michigan State University) join our group as a sabbatical visitor. (left on Mar. 23)
Prof. Cheol Ho Choi (Kyungpook National University) join our group as a visiging professor. (left on Feb. 1st)
Dr. Mori moved to RIKEN QBiC (Kobe).
The paper on the relationship between Ca2+-affinity and shielding of bulk water in
the Ca2+-pump has been published in PNAS.
Position opend for the Junior Research Associate (JRA) program in RIKEN. (closed)
The paper on the structural prediction of helical membrane proteins has been published in BMS Bioinformatics.
Assoc. chief scientist Dr. Yuji Sugita holds an additional post of the team leader of RIKEN AICS.
Assoc. chief scientist Dr. Yuji Sugita holds an additional post of the team leader of RIKEN QBiC.
Dr. Takashi Imai won the poster prize in CBI annual meeting 2010.
Dr. Takashi Imai has been honored by encouragement award of the Japan Association of Solution Chemistry.
The paper on the folding simulations of villin headpiece subdomain in explicit solvent has been published in Biophys. J.
The paper on the transition state structure for reversible phosphorylation reactions has been published in J.Comp.Chem.
Call for applications of Foreign Postdoctoral Researchers. (deadline: May 28)
Dr. Fumiko Ogushi won the poster award in 2nd Biosupercomputing symposium
Dr. Takashi Imai won the Research/Technology Encouragement Prize in RIKEN.
The paper on MP2 gradient in the generalized hybrid orbital QM/MM method has been published in J. Chem. Phys.
The paper on Pressure-Induced Protein Structural Transition and Water Penetration has been published in J. Phys. Chem. B.
The paper on the conformational changes of Sec translocon has been published in Biochemistry.
Dr. Pai-Chi Li has joined in our group.
Assoc. chief scientist Dr. Yuji Sugita won the 2009 Award of the Molecular Simulation Society of Japan.
The paper on the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase has been published in Chem.Phys.Lett.
Assoc. chief scientist Dr. Yuji Sugita has been honored by Morino foundation encouragement award for promoting fundamental researches of molecular science.
We have openings for Post-doctoral associates in our research group in the area of theoretical and computational chemistry and biophysics (see the web page).
Call for Applications for Special Postdoctoral Researchers and Foreign Postdoctoral Researchers.
(deadline:May 29,2009)
Dr. Andrei Pisliakov join our group as FPR.
The paper on the transmembrane structures of APP dimer has been published in JACS (Communication).
We have openings for Post-doctoral associates in our research group in the area of theoretical and computational chemistry and biophysics (see the web page).
The paper on the structure of SecYE translocon has been published in Nature. This work was done in collaboration with Prof. Nureki’s group in the University of Tokyo and Prof. Mori’s group in Kyoto University.
The paper on the MD simulation of MgtE has been published in PNAS. This work was done in collaboration with Prof. Ishitani in the University of Tokyo.
