A5029718850- Advanced Chemical Physics Studies
- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Computational Drug Discovery Methods
- DNA and Nucleic Acid Chemistry
- Crystallography and molecular interactions
- Molecular spectroscopy and chirality
- Radioactive element chemistry and processing
- Machine Learning in Materials Science
- Mass Spectrometry Techniques and Applications
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Photoreceptor and optogenetics research
- Photochemistry and Electron Transfer Studies
- Influenza Virus Research Studies
- Analytical Chemistry and Chromatography
- Lanthanide and Transition Metal Complexes
- Lipid Membrane Structure and Behavior
- Photosynthetic Processes and Mechanisms
- SARS-CoV-2 and COVID-19 Research
- Crystallization and Solubility Studies
- Various Chemistry Research Topics
- X-ray Diffraction in Crystallography
- Inorganic Fluorides and Related Compounds
- Molecular Junctions and Nanostructures
The University of Tokyo
2016-2025
Rikkyo University
2016-2025
Osaka University
2024
Japan Science Society
2016
Nagoya City University
2009-2014
Ehime University
2013
Kobe University
2006-2012
Japan Science and Technology Agency
2005-2011
Ritsumeikan University
2011
National Institute of Health Sciences
2008-2009
The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount works various fields have been made rather short period. Here, we report fragment molecular orbital (FMO) based interaction analysis on complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). target molecule was segmented into five fragments order capture site specific interactions with amino acid residues protease....
Abstract RNA‐based therapeutics is a promising approach for curing intractable diseases by manipulating various cellular functions. For eliciting RNA (i.e., mRNA and siRNA) functions successfully, the in extracellular space must be protected it delivered to cytoplasm. In this study, development of self‐degradable lipid‐like material that accelerate collapse lipid nanoparticles (LNPs) release into cytoplasm reported. The self‐degradability based on unique reaction “Hydrolysis accelerated...
A novel in silico drug design procedure is described targeting the Main protease (Mpro) of SARS-CoV-2 virus. The combines molecular docking, dynamics (MD), and fragment orbital (FMO) calculations. binding structure properties Mpro were predicted for Nelfinavir (NFV), which had been identified as a candidate compound through repositioning, Mpro. Several poses NFV complexes generated by from four docking selected scoring with FMO energy. Then, each pose was subjected to MD simulation, 100...
We have developed a visualized cluster analysis of protein−ligand interaction (VISCANA) that analyzes the pattern receptor and ligand on basis quantum theory for virtual screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319−324.) proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In FMO method, total energy molecule is evaluated summation energies interfragment (IFIEs). this paper, we...
The ab initio fragment molecular orbital calculations were performed for interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17β-estradiol (EST). interaction energies ligand at residue level calculated using HF and MP2 methods several basis sets. charge-transfer (CT) also analyzed based on configuration analysis interaction. Strong electrostatic observed between EST surrounding charged/polarized residues, Glu353, Arg394, His524, Thr347. Weak...
Abstract The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a and DNA duplex to elucidate their sequence‐specific binding stability of duplex, as determined by analysis inter‐ intramolecular interactions. Calculations AMBER94 force field at HF MP2 levels several basis sets. interfragment interaction energies (IFIEs) analyzed interactions CRP–cAMP each base pair, amino acid residue, pair residue. In addition, base–base...
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution: coupling with implicit solvent model based on Poisson–Boltzmann surface area called as FMO-PBSA. We investigated effects practical and heterogeneous targets uneven exposure to solvents unlike deoxyribonucleic acid our recent study. Interfragment interaction energy (IFIE) its decomposition analyses by FMO-PBSA revealed solvent-screening...
フラグメント分子軌道(Fragment Molecular Orbital; FMO)法はタンパク質などの巨大分子の電子状態計算を可能にする方法であり,FMO計算によって得られるフラグメント間相互作用エネルギー(Inter Fragment Interaction Energy; IFIE)がタンパク質-リガンド間相互作用などを理解する上で有用であるため創薬研究などに用いられている.本研究ではFMO計算プログラムABINIT-MP及びそのプリポストBioStation Viewerに,IFIEを静電相互作用エネルギー(ES),交換反発エネルギー(EX),電荷移動相互作用エネルギー(CT+mix),分散エネルギー(DI)の4つのエネルギー成分に分割・解析できる機能PIEDA (Pair Energy Decomposition...
ABSTRACT The spike protein of SARS‐CoV‐2 is a challenging target for theoretical approaches. Here we report benchmark calculation the droplet model by fragment molecular orbital (FMO) at second‐order Møller‐Plesset perturbation (MP2) level on supercomputer Fugaku. One hundred structure samples from dynamics (MD) simulations were used both closed and open forms this (PDB IDs 6XLU 6XM0 respectively). number total fragments about 20,000, job time per was 2 h 8 racks
Abstract We performed statistical interaction analysis using fragment molecular orbital (FMO) calculations on the droplet models of complexes formed between two popular mosquito repellents (DEET and Icaridin) target odorant binding protein Anopheles gambiae (AgamOBP1). These structure sets were generated by dynamics (MD) simulations, taking into account structural fluctuations under hydration. The different situation for was revealed; phenyl ring with π-electrons plays a leading role DEET,...
The fragmentation-based method has attracted interest to reduce the computational cost for quantum computation of chemistry. Previously (K. Sugisaki et al., J. Comput. Chem. 2024, 45, 2204), we reported simulation results variational eigensolver (VQE) unitary coupled cluster singles and doubles (UCCSD) under fragment molecular orbital (FMO) framework, where influence Trotter error was highlighted (FH)3 H2O-(FH)2 models. In this report, concurrent processing list is adapted with examples...
An important goal of mechanistic studies chemical reactions is to understand how atoms in reacting molecules behave at the molecular level. Toward this goal, full quantum mechanical dynamics (MD) simulations, which employed recently developed fragment orbital (FMO)-MD method, were carried out for hydrolysis methyl diazonium ion water. The simulations illustrated first time solvent water participate reaction and C−N bond cleavage O−C formation take place during reaction. It was revealed that...