Researcher Database

（Last updated : 2026-03-04 00:21:05）　

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TAKAHASHI Takuya

Department / Course College of Life Sciences Department of Bioinformatics

Title / Position Professor

Other Affiliations
1.	Graduate School of Life Sciences

Academic background
1.	1991/03 Degree Acquisition	│ The University of Tokyo Ph.D. in Science (The University of Tokyo)
2.	～1985	Department of Physics │ Faculty of Science │ The University of Tokyo │ Graduated
3.	～1991/03	Doctorial Course │ Graduate School, Division of Science │ The University of Tokyo │ Completed

Business career
1.	2010/04/01	Professor │ College of Life Sciences │ Ritsumeikan University
2.	2008/04/01 ～ 2010/03/31	Associate Professor │ College of Life Sciences │ Ritsumeikan University
3.	2003/04/01 ～ 2008/03/31	Associate Professor │ Graduate School of Scienceand Engineering │ Ritsumeikan University
4.	1997/09/01 ～ 2003/03/31	│ │ nins

Committee and society
1.	2014/01 ～ 2016/01	Japan Society for the Promotion of Science Grants-in-Aid forScientific Research

Research activities
1.		The Biophysical Society of Japan
2.		Protein Science Society of Japan

Research summary
Connecting Life Structure Information to Functional Information Based on enormous amount of observation data including DNA array and protein cubic structure, I will clarify the mechanisms of biometric structure formation and life function appearance, mainly using the approach in terms of theoretical calculation.

Present specialized field
Structural Biochemistry, Biophysics (Keyword：Structural biology, biophysics, molecular science, computer science)

Books
1.	2012/04	Practical Estimation of TCR-pMHC Binding Free-Energy Based on the Dielectric Model and the Coarse-Grained Model │ ,pp.107-134

Papers
1.	2026/01/11	Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method │ Scientific Reports │
2.	2025/05/28	Conserved structural topologies in RNase A-like and trypsin-like serine proteases: a sequence-based folding analysis │ BMC Molecular and Cell Biology │ 26 (16)
3.	2025/04/26	A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape │ Biophysics and Physicobiology │ 22
4.	2023/04/11	Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region │ ACS OMEGA │ 8 (16),pp.14572-14582
5.	2023/04/06	Carbon nanotube recognition by human Siglec-14 provokes inflammation │ nature nanotechnology │ 18,pp.628-636
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Academic conference presentation
1.	2024/06/25	Development of drug discovery platform technology based on a generalized-ensemble simulation method -Evaluation of SARS CoV-2 PLpro candidate inhibitors-
2.	2024/06/25	Investigations of hydration structures and dynamics around proteins and peptides with MD simulations
3.	2024/06/25	The effect of the 2-OH group of ceramide in Arabidopsis thaliana on plant cell membranes using MD simulation
4.	2024/06/25	Verification of the effect of ligand and receptor flexibility on inhibitory activity by MD simulation
5.	2023/11/14	Elucidation of hydration dynamics around peptides and proteins by molecular dynamics simulation
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Achievements of joint.Funded research
1.	2024/04/01 ～ 2025/03/31	Comprehensive exploration of the binding modes of SARS CoV-2 PLpro and ligands using mD-VcMD

Subject
1.	数値シミュレーション実験
2.	生命情報学基礎演習1

Message
1.	Linking biological structure information with functional information: Elucidation of formation of three-dimensional structure of biomolecules, and elucidation of how functions are expressed from three-dimensional structure information. Living organisms are composed of tissues, cells, intracellular organelles, etc. Biological phenomena are realized through various functions of enormous biopolymers constituting these living tissues. Specifically, enzymes in solution in the living body have a function to control complex biological reactions through a specific three-dimensional structure, and ion channels in the biological membrane control transmission and accumulation of various ions , Involved in information processing and intracellular signaling in the brain, basic information for determining its three-dimensional structure is stored in DNA. With the recent progress in analysis technology of DNA sequence information and protein three-dimensional structure information, enormous amounts of primary structure data and tertiary structure data have been clarified, and the rapid development of bioinformatics is expected there. In my laboratory, in order to elucidate the formation of a three-dimensional structure from this primary structure information and to clarify how the function is expressed from the three-dimensional structure information, a method such as simulation or energy calculation Use it to study. Various methods such as informatical methods such as construction of physicochemical theory based on experimental data, database analysis etc., various molecular simulation, quantum chemical calculation, approximate calculation using continuum model are used.

Home Page
http://www.ritsumei.ac.jp/~tkhs/index_e.html