Shigenori Tanaka

Kobe University
Graduate School of System Informatics
Department of Computational Science
1-1, Rokkodai, Nada, Kobe 657-8501, Japan
TEL: +81-78-803-6620
FAX: +81-78-803-6620
E-MAIL: tanaka2[at]kobe-u.ac.jp

Research Topics

First-Principles Biomolecular Simulations

We are developing computational methodologies for ab initio calculations of biomolecular systems on the basis of fragment molecular orbital (FMO) method. The FMO method currently provides a state-of-the-art tool for the electronic structure calculations of proteins and nucleic acids, and has enabled us to perform a variety of first-principles biomolecular simulations. Examples for target systems include nuclear receptors, influenza viral proteins, SARS-CoV-2 viral proteins, bioluminescent proteins, and DNA-protein complexes.

[Selected Publications]

・K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Nakano, and S. Tanaka, “Intra- and Inter-Molecular Interactions between Cyclic-AMP Receptor Protein and DNA: Ab Initio Fragment Molecular Orbital Study”, J. Comput. Chem. 27 (2006) pp. 948-960.
・M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, “Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator. Part II: Influence of Mutations in Transcriptional Activation Function 2 Activating Domain Core on the Molecular Interactions”, J. Phys. Chem. A 112 (2008) pp. 1986-1998.
・A. Tagami, N. Ishibashi, D. Kato, N. Taguchi, Y. Mochizuki, H. Watanabe, M. Ito, and S. Tanaka, “Ab Initio Quantum-Chemical Study on Emission Spectra of Bioluminescent Luciferases by Fragment Molecular Orbital Method”, Chem. Phys. Lett. 472 (2009) pp. 118-123.
・T. Iwata, K. Fukuzawa, K. Nakajima, S. Aida-Hyugaji, Y. Mochizuki, H. Watanabe, and S. Tanaka, “Theoretical Analysis of Binding Specificity of Influenza Viral Hemagglutinin to Avian and Human Receptors Based on the Fragment Molecular Orbital Method”, Comput. Biol. Chem. 32 (2008) pp. 198-211.
・K. Takematsu, K. Fukuzawa, K. Omagari, S. Nakajima, K. Nakajima, Y. Mochizuki, T. Nakano, H. Watanabe, and S. Tanaka, “Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding”, J. Phys. Chem. B 113 (2009) pp. 4991-4994.
・A. Yoshioka, K. Fukuzawa, Y. Mochizuki, K. Yamashita, T. Nakano, Y. Okiyama, E. Nobusawa, K. Nakajima, and S. Tanaka, “Prediction of Probable Mutations in Influenza Virus Hemagglutinin Protein Based on Large-Scale Ab Initio Fragment Molecular Orbital Calculations”, J. Mol. Graph. Model. 30 (2011) pp. 110-119.
・S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama, and K. Fukuzawa, “Electron-Correlated Fragment-Molecular-Orbital Calculations for Biomolecular and Nano Systems”, Phys. Chem. Chem. Phys. 16 (2014) pp. 10310-10344.
・R. Hatada, K. Okuwaki, Y. Mochizuki, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and S. Tanaka, “Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7)”. J. Chem. Inf. Model. 60 (2020) pp. 3593-3602.
・K. Fukuzawa and S. Tanaka, “Fragment Molecular Orbital Calculations for Biomolecules”, Curr. Opin. Struct. Biol. 72 (2022) pp. 127-134.

In Silico Drug Design

Structure-based simulation is a promising approach to rational drug design. We have developed a variety of multi-scale computational schemes on the basis of fragment molecular orbital, molecular dynamics, and coarse-grained methods.

[Selected Publications]

・Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, and S. Tanaka, “Application of the Fragment Molecular Orbital Method for Determination of Atomic Charges on Polypeptides. II. Toward an Improvement of Force Fields Used for Classical Molecular Dynamics Simulations”, Chem. Phys. Lett. 467 (2009) pp. 417-423.
・C. Watanabe, H. Watanabe, and S. Tanaka, “An Interpretation of Positional Displacement of the Helix12 in Nuclear Receptors: Preexistent Swing-up Motion Triggered by Ligand Binding”, Biochim. Biophys. Acta 1804 (2010) pp. 1832-1840.
・T. Nakano, Y. Mochizuki, K. Yamashita, C. Watanabe, K. Fukuzawa, K. Segawa, Y. Okiyama, T. Tsukamoto, and S. Tanaka, “Development of the Four-Body Corrected Fragment Molecular Orbital (FMO4) Method”, Chem. Phys. Lett. 523 (2012) pp. 128-133.
・C. Watanabe, K. Fukuzawa, Y. Okiyama, T. Tsukamoto, A. Kato, S. Tanaka, Y. Mochizuki, and T. Nakano, “Three- and Four-Body Corrected Fragment Molecular Orbital Calculations with a Novel Subdividing Fragmentation Method Applicable to Structure-Based Drug Design”, J. Mol. Graph. Model. 41 (2013) pp. 31-42.
・S. Uehara and S. Tanaka, “AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking”, Molecules 21 (2016) 1604.
・S. Uehara and S. Tanaka, “Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations”, J. Chem. Inf. Model. 57 (2017) pp. 742-756.
・Y. Okiyama, T. Nakano, C. Watanabe, K. Fukuzawa, Y. Mochizuki, and S. Tanaka, “Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study”, J. Phys. Chem. B 122 (2018) pp. 4457-4471.
・Y. Okiyama, C. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, “Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies”, J. Phys. Chem. B 123 (2019) pp 957-973.
・S. Nakata, Y. Mori, and S. Tanaka, “End-to-End Protein-Ligand Complex Structure Generation with Diffusion-Based Generative Models”, BMC Bioinformatics 24 (2023) 233.

Energy Conversion in Biomolecular Systems

Protein systems contain a variety of interesting dynamical behaviors intimately associated with their functions. Some of them play essential roles for high-efficiency energy conversions or signal transductions in bio-systems. We have developed analytical and computational tools for describing protein dynamics such as vibrational energy transfer, excitation energy transfer and charge transfer.

[Selected Publications]

・S. Tanaka, “Renormalization-Group Inspired Approach to Vibrational Energy Transfer in Protein”, J. Phys. Soc. Jpn. 81 (2012) 033801.
・S. Tanaka, “Modulation of Excitation Energy Transfer by Conformational Oscillations in Biomolecular Systems”, Chem. Phys. Lett. 508 (2011) pp. 139-143.
・Y. Suzuki and S. Tanaka, “Excitation Energy Transfer Modulated by Oscillating Electronic Coupling of a Dimeric System Embedded in a Molecular Environment”, Phys. Rev. E 86 (2012) 021914.
・S. Tanaka and E.B. Starikov, “Analysis of Electron-Transfer Rate Constant in Condensed Media with Inclusion of Inelastic Tunneling and Nuclear Quantum Effects”, Phys. Rev. E 81 (2010) 027101.
・T. Matsuoka, S. Tanaka, and K. Ebina, “Hierarchical Coarse-Graining Model for Photosystem II Including Electron and Excitation-Energy Transfer Processes”, BioSystems 117 (2014) pp. 15-29.
・Y. Suzuki, K. Ebina, and S. Tanaka, “Four-Electron Model for Singlet and Triplet Excitation Energy Transfers with Inclusion of Coherence Memory, Inelastic Tunneling and Nuclear Quantum Effects”, Chem. Phys. 474 (2016) pp. 18-24.


We have developed a theoretical method to describe correlational properties of liquid water on the basis of integral equation approach in which triplet correlations and associated bridge functions are taken into account in the framework of density functional theory.

[Selected Publications]

・S. Tanaka and M. Nakano, “Triplet Correlations and Bridge Functions in Classical Density Functional Theory for Liquid Water”, Chem. Phys. Lett. 572 (2013) pp. 38-43.
・S. Tanaka and M. Nakano, “Classical Density Functional Calculation of Radial Distribution Functions of Liquid Water”, Chem. Phys. 430 (2014) pp. 18-22.

Quantum Monte Carlo

We have developed novel methods for quantum Monte Carlo (QMC) calculations for molecular and condensed-matter systems. Variational and path-integral QMC methods have been implemented and applied to water molecule, NiO, and small peptides.

[Selected Publications]

・S. Tanaka, S.M. Rothstein, and W.A. Lester, Jr., ed., “Advances in Quantum Monte Carlo” (ACS Symposium Series 1094, American Chemical Society, Washington, DC, 2012).
・W.A. Lester, Jr., S.M. Rothstein, and S. Tanaka, ed., “Recent Advances in Quantum Monte Carlo Methods , Part II” (World Scientific, Singapore, 2002).
・S. Tanaka, “Cohesive Energy of NiO: A Quantum Monte Carlo Approach”, J. Phys. Soc. Jpn. 62, No. 6 (1993) pp. 2112-2119.
・S. Tanaka, “Variational Quantum Monte Carlo Approach to the Electronic Structure of NiO”, J. Phys. Soc. Jpn. 64, No. 11 (1995) pp. 4270-4277.
・S. Tanaka, “Structural Optimization in Variational Quantum Monte Carlo”, J. Chem. Phys. 100, No. 10 (1994) pp. 7416-7420.
・R. Maezono, H. Watanabe, S. Tanaka, M.D. Towler, and R.J. Needs, “Fragmentation Method Combined with Quantum Monte Carlo Calculations”, J. Phys. Soc. Jpn. 76, No.6 (2007) 064301.
・T. Fujita, S. Tanaka, T. Fujiwara, M. Kusa, Y. Mochizuki, and M. Shiga, “Ab Initio Path Integral Monte Carlo Simulations for Water Trimer with Electron Correlation Effects”, Comput. Theor. Chem. 997 (2012) pp. 7-13.
・S. Tanaka, “Variational Quantum Monte Carlo with Inclusion of Orbital Correlations”, J. Phys. Soc. Jpn. 82, No.7 (2013) 075001.

Quantum Many-Body Systems

One of my longstanding interests is laid on quantum many-body problems. Examples include the theoretical analyses of correlational, thermodynamic and transport properties of electron liquids and hydrogen plasmas over wide ranges of density and temperature. I have also calculated the multiparticle distribution functions for ideal Fermi gas system in the ground state for any spatial dimension. The N-particle distribution function is expressed in terms of a determinant form in which a correlation kernel plays a vital role. The expression obtained for the one-dimensional Fermi gas is essentially equivalent to that known for the distribution of the eigenvalues of random unitary matrices, which, in turn, has a mathematical structure analogous to the distribution of non-trivial zeros of the Riemann zeta function.

[Selected Publications]

・S. Tanaka and S. Ichimaru, “Thermodynamics and Correlational Properties of Finite-Temperature Electron Liquids in the Singwi-Tosi-Land-Sjolander Approximation”, J. Phys. Soc. Jpn. 55, No. 7 (1986) pp. 2278-2289.
・S. Ichimaru, H. Iyetomi, and S. Tanaka, “Statistical Physics of Dense Plasmas: Thermodynamics, Transport Coefficients and Dynamic Correlations”, Phys. Rep. 149, Nos. 2-3 (1987) pp. 91-205.
・S. Tanaka and S. Ichimaru, “Spin-Dependent Correlations and Thermodynamic Functions for Electron Liquids at Arbitrary Degeneracy and Spin Polarization”, Phys. Rev. B39 (1989) pp. 1036-1051.
・S. Tanaka, X.-Z. Yan, and S. Ichimaru, “Equation of State and Conductivities of Dense Hydrogen Plasmas near the Metal-Insulator Transition”, Phys. Rev. A41 (1990) pp. 5616-5625.
・S. Tanaka, “Multiparticle Distributions of Ideal Fermi Gas: Analogy to Random Matrices and the Riemann Zeros”, J. Phys. Soc. Jpn. 80 (2011) 034001.
・S. Tanaka, “Correlational and Thermodynamic Properties of Finite-Temperature Electron Liquids in the Hypernetted-Chain Approximation”, J. Chem. Phys. 145 (2016) 214104.