Shoji Takada

Shoji Takada, Do Hyun Kim, Seung Yup Lee, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Reactor core design of gas Turbine High Temperature Reactor 300

Kazuhiko Kunitomi, Xing Yan, Shoji Katanishi, 2004 .

Protein‐specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions

Le Chang, Takeshi Ishikawa, Shoji Takada, 2013, J. Comput. Chem..

Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

Shoji Takada, Ryo Kanada, Takeshi Kuwata, 2013, PLoS Comput. Biol..

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

Shoji Takada, Giovanni B Brandani, S. Takada, 2018, bioRxiv.

1P-145 Simulation study on stepping mechanism of Conventional Kinesin by coarse-grained model(The 46th Annual Meeting of the Biophysical Society of Japan)

Shoji Takada, Ryo Kanada, Kei-ichi Okazaki, 2008 .

C308 RESEARCH AND DEVELOPMENT FOR GAS TURBINE SYSTEM IN GTHTR300

Kazuhiko Kunitomi, Xing Yan, Shoji Katanishi, 2003 .

Faculty Opinions recommendation of Insights into protein folding mechanisms from large scale analysis of mutational effects.

Shoji Takada, 2010 .

ICONE11-36368 THE 1/3-SCALE AERODYNAMICS PERFORMANCE TEST OF HELIUM COMPRESSOR FOR GTHTR300 TURBO MACHINE OF JAERI (STEP 1)

Kazuhiko Kunitomi, Kunio Takahashi, Xing Yan, 2003 .

Improvement of Temperature Evaluation Model of Biological Shielding Concrete for HTTR Test Simulating LOFC With VCS Inactive

Shoji Takada, Masato Ono, Kazuhiro Sawa, 2013 .

Development of operation and maintenance technology for HTGRs by using HTTR (High Temperature engineering Test Reactor)

Shoji Takada, Masayuki Shinozaki, Atsushi Shimizu, 2014 .

Evaluation of aseismic integrity in the HTTR core-bottom structure V. On the static and dynamic behavior of graphitic HTTR key-keyway structures

Shoji Takada, Tatsuo Iyoku, Masatoshi Futakawa, 1996 .

Evaluation of aseismic integrity in HTTR core-bottom structure II. Vibrational characteristics of keyed graphite components

Shoji Takada, Tatsuo Iyoku, Hiroshi Shirai, 1994 .

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously.

Shoji Takada, Wenfei Li, 2009, The Journal of chemical physics.

Design Improvements of Power Conversion System of Gas Turbine High Temperature Reactor (GTHTR300)

Kazuhiko Kunitomi, Xing Yan, Shoji Takada, 2004 .

JCP Special Topic: Multidimensional Spectroscopy

Shoji Takada, Shaul Mukamel, Shinji Saito, 2015 .

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

Shoji Takada, Hiroo Kenzaki, S. Takada, 2015, PLoS Comput. Biol..

ICONE11-36369 A VERIFICATION PLAN OF ROTOR DYNAMICS OF TURBOMACHINE SYSTEM SUPPORTED BY AMB FOR THE GTHTR300 (STEP 1)

Isao Minatsuki, Yorikata Mizokami, Kazuhiko Kunitomi, 2003 .

ICONE23-1636 Investigation of Characteristics of Natural Circulation of Water in Vessel Cooling System in Loss of Core Cooling Test without Nuclear Heating

Shigeaki Nakagawa, Shoji Takada, Kazuhiro Sawa, 2015 .

R&D on the power conversion system for gas turbine high temperature reactors

Kazuhiko Kunitomi, Xing Yan, Shoji Katanishi, 2004 .

ICONE23-1670 DEVELOPMENT OF THE PREDICTION TECHNOLOGY OF CABLE DISCONNECTION OF IN-CORE NEUTRON DETECTOR FOR THE FUTURE HIGH-TEMPERATURE GAS COOLED REACTORS

Shoji Takada, Yuki Honda, Kazuhiro Sawa, 2015 .

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

Shoji Takada, Tomohiro Tanaka, Naoto Hori, 2015, PLoS Comput. Biol..

Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

Shoji Takada, Shintaroh Kubo, Suguru Kato, 2020, Scientific Reports.

Negative design of foldable proteins : new algorithm

Shoji Takada, W. Jin, Y. Fujitsuka, 2003 .

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations

Shoji Takada, Wenfei Li, Shintaroh Kubo, 2017, PLoS Comput. Biol..

Early Research in Biophysics Award—Report on the Fourteenth Award Selection Process—: ―第14回選考過程報告―

Shoji Takada, Akihiko Ishijima, Yoko Y. Toyoshima, 2018 .

Research and Development for Gas Turbine System in GTHTR300

Kazuhiko Kunitomi, Xing Yan, Shoji Katanishi, 2004 .

Safety evaluation method of the GTHTR300

Kazuhiko Kunitomi, Shoji Katanishi, Shoji Takada, 2004 .

SimFold energy function for de novo protein structure prediction: Consensus with Rosetta

Shoji Takada, George Chikenji, Yoshimi Fujitsuka, 2005, Proteins.

A Safety Evaluation of HTTR Core Components Against 2011 Tohoku Earthquake

Shoji Takada, Masato Ono, Kazuhiro Sawa, 2013 .

A Reversible Fragment Assembly Method for De Novo Protein Structure Prediction

Shoji Takada, George Chikenji, Yoshimi Fujitsuka, 2003 .

Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

Shoji Takada, Shintaroh Kubo, Suguru Kato, 2020, Scientific reports.

Faculty Opinions recommendation of New scenarios of protein folding can occur on the ribosome.

Shoji Takada, 2011 .

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study

Shoji Takada, Giovanni B. Brandani, Cheng Tan, 2021, PLoS Comput. Biol..

Variational Theory for Site Resolved Protein Folding Free Energy Surfaces

Shoji Takada, John J. Portman, Peter G. Wolynes, 1998, cond-mat/9805366.

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations.

Shigehiko Hayashi, Shoji Takada, Matthew J. McGrath, 2013, Journal of the American Chemical Society.

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

Shoji Takada, John J. Portman, Peter G. Wolynes, 2000, cond-mat/0008455.

Roles of physical interactions in determining protein‐folding mechanisms: Molecular simulation of protein G and α spectrin SH3

Shoji Takada, Yoshimi Fujitsuka, Seung Yup Lee, 2004, Proteins.

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

Shoji Takada, Sotaro Fuchigami, Toru Niina, 2019 .

Glassy Dynamics of Random Heteropolymers

Shoji Takada, Peter G. Wolynes, 1997 .

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins.

Shoji Takada, Tsuyoshi Terakawa, S. Takada, 2014, Journal of chemical theory and computation.

Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.

Shoji Takada, Wenfei Li, S. Takada, 2010, Biophysical journal.

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

Shoji Takada, Wei Wang, Tsuyoshi Terakawa, 2012, Proceedings of the National Academy of Sciences.

Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain.

Shoji Takada, Tsuyoshi Terakawa, S. Takada, 2011, Biophysical journal.

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

Shoji Takada, Wei Wang, Wenfei Li, 2014, Proceedings of the National Academy of Sciences.

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

Shoji Takada, Ryo Kanada, Tsuyoshi Terakawa, 2015, Accounts of chemical research.

Guiding the search for a protein's maximum rate of folding

Jeffery G. Saven, Shoji Takada, Ting Wang, 2004 .

Folding energy landscape and network dynamics of small globular proteins

Shoji Takada, Naoto Hori, George Chikenji, 2009, Proceedings of the National Academy of Sciences.

Wentzel–Kramers–Brillouin theory of multidimensional tunneling: General theory for energy splitting

Shoji Takada, Hiroki Nakamura, S. Takada, 1994 .

Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes.

Shoji Takada, Masahiro Shimizu, S. Takada, 2018, Journal of chemical theory and computation.

Molecular Dynamics Simulations of Biomolecules

Shoji Takada, S. Takada, 2013 .

p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains.

Shoji Takada, Tsuyoshi Terakawa, Hiroo Kenzaki, 2012, Journal of the American Chemical Society.

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.

Shoji Takada, Ryo Kanada, Tsuyoshi Terakawa, 2019, Biophysical journal.

Effects of vibrational excitation on multidimensional tunneling: General study and proton tunneling in tropolone

Shoji Takada, Hiroki Nakamura, S. Takada, 1995 .

Secondary structure provides a template for the folding of nearby polypeptides

Shoji Takada, Tomoshi Kameda, S. Takada, 2006, Proceedings of the National Academy of Sciences.

Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations.

Shoji Takada, Kei-ichi Okazaki, S. Takada, 2011, Structure.

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

Shoji Takada, Le Chang, S. Takada, 2016, Scientific Reports.

Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

Shoji Takada, John J. Portman, Peter G. Wolynes, 2000, cond-mat/0008454.

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations.

Shoji Takada, Sotaro Fuchigami, Toru Niina, 2020, Journal of chemical theory and computation.

Optimizing physical energy functions for protein folding

Shoji Takada, Peter G Wolynes, Yoshimi Fujitsuka, 2003, Proteins.

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights

Shoji Takada, Masahiro Shimizu, Yukari Sakiyama, 2016, Proceedings of the National Academy of Sciences.

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase.

Shoji Takada, Nobuyasu Koga, S. Takada, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox

Shoji Takada, George Chikenji, Yoshimi Fujitsuka, 2004 .

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

Shoji Takada, Nobuyasu Koga, Tomoshi Kameda, 2009, Proceedings of the National Academy of Sciences.

Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop.

Shoji Takada, Chigusa Kobayashi, S. Takada, 2006, Biophysical journal.

Folding coupled with assembly in split green fluorescent proteins studied by structure-based molecular simulations.

Shoji Takada, Mashiho Ito, Takeaki Ozawa, 2013, The journal of physical chemistry. B.

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

Shoji Takada, Toru Niina, Giovanni B Brandani, 2018, Nucleic acids research.

Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations.

Shoji Takada, Akira R Kinjo, S. Takada, 2003, Biophysical journal.

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

Shoji Takada, Takuya Ueda, Hideki Taguchi, 2009, Proceedings of the National Academy of Sciences.

Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

Shoji Takada, Xin-Qiu Yao, Satoshi Murakami, 2010, Nature communications.

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations

Shoji Takada, Nobuyasu Koga, Fumiko Takagi, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics.

Shoji Takada, Tsuyoshi Terakawa, Cheng Tan, 2016, Journal of the American Chemical Society.