All Stories

  1. Impact of Nucleotide Flexibility on Aptamer–Protein Recognition: RNA vs RNA–DNA Chimera

    Article • ACS Chemical Biology, April 2026, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  2. One-pot synthesis of trifluoromethyl ketone-containing heterocycles via tandem photocatalytic haloalkylation of olefins and intramolecular cyclisation

    Article • New Journal of Chemistry, January 2026, Royal Society of Chemistry

    Dr Takeshi Ishikawa

  3. Photoredox‐Catalyzed α‐Arylation of Bromotrifluoroacetone with Electron‐Rich (Hetero)Arenes

    Article • ChemistrySelect, May 2025, Wiley

    Dr Takeshi Ishikawa

  4. Extension of the K-orbital method and its demonstration in conjunction with spin-adapted large-scale parallelized complete active space configuration interaction

    Article • Chemistry Letters, May 2025, Oxford University Press (OUP)

    Dr Takeshi Ishikawa

  5. In Silico Discovery of SARS-CoV-2 Main Protease Inhibitors Using Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

    Article • The Journal of Physical Chemistry, January 2025, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  6. Visualization of Interfacial Electrostatic Complementarity Reveals Evolutionary Changes in SARS-CoV-2 RBD–hACE2 Interactions

    Article • Physical Chemistry Chemical Physics, January 2025, Royal Society of Chemistry

    Dr Takeshi Ishikawa

  7. Sulfoquinovosyl diacylglycerol, a component of Holy Basil Ocimum tenuiflorum, inhibits the activity of the SARS-CoV-2 main protease and viral replication in vitro

    Article • Journal of Natural Medicines, November 2024, Springer Science + Business Media

    Dr Takeshi Ishikawa

  8. Quantum Chemistry-Based Protein–Protein Docking without Empirical Parameters

    Article • Journal of Chemical Theory and Computation, June 2024, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  9. Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain

    Article • Carbohydrate Polymer Technologies and Applications, June 2024, Elsevier

    Dr Takeshi Ishikawa

  10. A facile access to aliphatic trifluoromethyl ketones via photocatalyzed cross-coupling of bromotrifluoroacetone and alkenes

    Article • Organic & Biomolecular Chemistry, January 2024, Royal Society of Chemistry

    Dr Takeshi Ishikawa

  11. Nucleophilic fluorine substitution reaction of α-carbonyl benzyl bromide, phenylthiofluoroalkyl bromide, and 2-bromo-2-phenoxyacetonitrile

    Article • RSC Advances, January 2024, Royal Society of Chemistry

    Dr Takeshi Ishikawa

  12. Reaction Mechanism and Origin of Stereoselectivity in the Fluorination and Trifluoromethylthiolation of 2‐Bromoamides with AgF and AgSCF3

    Article • European Journal of Organic Chemistry, December 2023, Wiley

    Dr Takeshi Ishikawa

  13. Alkyl gallates inhibit serine O-acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics

    Article • Frontiers in Microbiology, October 2023, Frontiers

    Dr Takeshi Ishikawa

  14. Insights into the molecular interaction of cyclodextran with a guest molecule: A computational study

    Article • Carbohydrate Polymers, February 2023, Elsevier

    Dr Takeshi Ishikawa

  15. Quantification and Neutralization of the Interfacial Electrostatic Potential and Visualization of the Dispersion Interaction in Visualization of the Interfacial Electrostatic Complementarity

    Article • The Journal of Physical Chemistry, October 2022, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  16. Correction to “Discovery and Structure-Based Optimization of Novel Atg4B Inhibitors for the Treatment of Castration-Resistant Prostate Cancer”

    Article • Journal of Medicinal Chemistry, May 2022, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  17. Correction to “Trifluoromethylthiolation of Hindered α-Bromoamides with Nucleophilic Trifluoromethylthiolating Reagents”

    Article • The Journal of Organic Chemistry, March 2022, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  18. Discovery and Structure-Based Optimization of Novel Atg4B Inhibitors for the Treatment of Castration-Resistant Prostate Cancer

    Article • Journal of Medicinal Chemistry, March 2022, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  19. Lead Optimization of Influenza Virus RNA Polymerase Inhibitors Targeting PA–PB1 Interaction

    Article • Journal of Medicinal Chemistry, December 2021, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  20. Trifluoromethylthiolation of Hindered α-Bromoamides with Nucleophilic Trifluoromethylthiolating Reagents

    Article • The Journal of Organic Chemistry, December 2021, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  21. Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity

    Article • The Journal of Physical Chemistry Letters, November 2021, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  22. Visualization of the Interfacial Electrostatic Complementarity: A Method for Analysis of Protein–Protein Interaction Based on Ab Initio Quantum Chemical Calculations

    Article • Journal of Chemical Theory and Computation, August 2021, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  23. The Antiviral Effect of the Chemical Compounds Targeting DED/EDh Motifs of the Viral Proteins on Lymphocytic Choriomeningitis Virus and SARS-CoV-2

    Article • Viruses, June 2021, MDPI AG

    Dr Takeshi Ishikawa

  24. Cover Feature: Silver‐Promoted Fluorination Reactions of α‐Bromoamides (Chem. Eur. J. 19/2021)

    Article • Chemistry - A European Journal, January 2021, Wiley

    Dr Takeshi Ishikawa

  25. Silver‐Promoted Fluorination Reactions of α‐Bromoamides

    Article • Chemistry - A European Journal, January 2021, Wiley

    Dr Takeshi Ishikawa

  26. FMO Interfaced with Molecular Dynamics Simulation

    Article • January 2021, Springer Science + Business Media

    Dr Takeshi Ishikawa

  27. PAICS: Development of an Open-Source Software of Fragment Molecular Orbital Method for Biomolecule

    Article • January 2021, Springer Science + Business Media

    Dr Takeshi Ishikawa

  28. The ABINIT-MP Program

    Article • January 2021, Springer Science + Business Media

    Dr Takeshi Ishikawa

  29. A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method

    Article • Chemical Physics Letters, December 2020, Elsevier

    Dr Takeshi Ishikawa

  30. Novel and potent antimicrobial effects of caspofungin on drug-resistant Candida and bacteria

    Article • Scientific Reports, October 2020, Springer Science + Business Media

    Dr Takeshi Ishikawa, Takahiro Takazono

  31. Novel Compounds Identified by Structure-Based Prion Disease Drug Discovery Using In Silico Screening Delay the Progression of an Illness in Prion-Infected Mice

    Article • Neurotherapeutics, October 2020, Elsevier

    Dr Takeshi Ishikawa

  32. A Quinolinone Compound Inhibiting the Oligomerization of Nucleoprotein of Influenza A Virus Prevents the Selection of Escape Mutants

    Article • Viruses, March 2020, MDPI AG

    Dr Takeshi Ishikawa

  33. Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation

    Article • Chemical Physics Letters, October 2019, Elsevier

    Dr Takeshi Ishikawa

  34. Characterization of Entamoeba histolytica adenosine 5′-phosphosulfate (APS) kinase; validation as a target and provision of leads for the development of new drugs against amoebiasis

    Article • PLoS Neglected Tropical Diseases, August 2019, PLOS

    Dr Takeshi Ishikawa, Fumika Mi-ichi

  35. Roles of YIGL sequence of Ebola virus VP40 on genome replication and particle production

    Article • Journal of General Virology, July 2019, Society for General Microbiology

    Dr Takeshi Ishikawa

  36. A designer molecular chaperone against transmissible spongiform encephalopathy slows disease progression in mice and macaques

    Article • Nature Biomedical Engineering, February 2019, Springer Science + Business Media

    Dr Takeshi Ishikawa

  37. Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance

    Article • EBioMedicine, January 2019, Elsevier

    Dr Takeshi Ishikawa

  38. Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations

    Article • Journal of Chemical Information and Modeling, December 2018, American Chemical Society (ACS)

    Dr Takeshi Ishikawa, Professor Yasuteru Shigeta

  39. RI-MP3 calculations of biomolecules based on the fragment molecular orbital method

    Article • Journal of Computational Chemistry, September 2018, Wiley

    Dr Takeshi Ishikawa

  40. Fragment Molecular Orbital Study of the Interaction between Sarco/Endoplasmic Reticulum Ca2+-ATPase and its Inhibitor Thapsigargin toward Anti-Malarial Development

    Article • The Journal of Physical Chemistry, August 2018, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  41. Identification of Alprenolol Hydrochloride as an Anti-prion Compound Using Surface Plasmon Resonance Imaging

    Article • Molecular Neurobiology, April 2018, Springer Science + Business Media

    Dr Takeshi Ishikawa

  42. Ab initio quantum chemical calculation of electron density, electrostatic potential, and electric field of biomolecule based on fragment molecular orbital method

    Article • International Journal of Quantum Chemistry, November 2017, Wiley

    Dr Takeshi Ishikawa

  43. Age of donor of human mesenchymal stem cells affects structural and functional recovery after cell therapy following ischaemic stroke

    Article • Journal of Cerebral Blood Flow & Metabolism, September 2017, SAGE Publications

    Dr Takeshi Ishikawa, Yoichi Morofuji

  44. Structure-based drug discovery for combating influenza virus by targeting the PA–PB1 interaction

    Article • Scientific Reports, August 2017, Springer Science + Business Media

    Dr Takeshi Ishikawa

  45. Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase

    Article • Drug Metabolism and Pharmacokinetics, August 2017, Elsevier

    Dr Takeshi Ishikawa

  46. Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches

    Article • PLOS One, March 2017, PLOS

    Dr Takeshi Ishikawa

  47. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase

    Article • The Journal of Physical Chemistry, October 2016, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  48. Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation

    Article • Journal of Computer-Aided Molecular Design, September 2016, Springer Science + Business Media

    Dr Takeshi Ishikawa

  49. Structure-Based Drug Discovery for Prion Disease Using a Novel Binding Simulation

    Article • EBioMedicine, July 2016, Elsevier

    Dr Takeshi Ishikawa

  50. A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1–N9 Neuraminidases: Insight into Neuraminidase–Inhibitor Interactions

    Article • Journal of Medicinal Chemistry, May 2016, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  51. Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor

    Article • Scientific Reports, March 2016, Springer Science + Business Media

    Dr Takeshi Ishikawa

  52. Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex

    Article • Nature Communications, January 2016, Springer Science + Business Media

    Dr Takeshi Ishikawa

  53. Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation

    Article • Chemical Physics, September 2015, Elsevier

    Dr Takeshi Ishikawa

  54. Molecular cloning and biochemical characterization of isoprene synthases from the tropical trees Ficus virgata, Ficus septica, and Casuarina equisetifolia

    Article • Journal of Plant Research, June 2015, Springer Science + Business Media

    Dr Takeshi Ishikawa

  55. A Mini-review on Chemoinformatics Approaches for Drug Discovery

    Article • Journal of Computer Aided Chemistry, January 2015, Division of Chemical Information and Computer Sciences

    Dr Takeshi Ishikawa

  56. Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions

    Article • Journal of Computational Chemistry, February 2013, Wiley

    Dr Takeshi Ishikawa

  57. A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation

    Article • Bulletin of the Chemical Society of Japan, February 2013, The Chemical Society of Japan

    Dr Takeshi Ishikawa

  58. Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

    Article • Chemical Physics Letters, February 2013, Elsevier

    Dr Takeshi Ishikawa

  59. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Dr Yuji O. Kamatari, Dr Takeshi Ishikawa

  60. RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital Method

    Article • The Journal of Physical Chemistry Letters, January 2012, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  61. Partial energy gradient based on the fragment molecular orbital method: Application to geometry optimization

    Article • Chemical Physics Letters, November 2010, Elsevier

    Dr Takeshi Ishikawa

  62. Interaction Analysis of the Native Structure of Prion Protein with Quantum Chemical Calculations

    Article • Journal of Chemical Theory and Computation, February 2010, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  63. Acceleration of monomer self-consistent charge process in fragment molecular orbital method

    Article • Chem-Bio Informatics Journal, January 2010, Chem-Bio Informatics Society

    Dr Takeshi Ishikawa

  64. Theoretical study of the prion protein based on the fragment molecular orbital method

    Article • Journal of Computational Chemistry, December 2009, Wiley

    Dr Takeshi Ishikawa

  65. Fragment molecular orbital calculation using the RI-MP2 method

    Article • Chemical Physics Letters, May 2009, Elsevier

    Dr Takeshi Ishikawa

  66. Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)

    Article • The Journal of Physical Chemistry, January 2009, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  67. Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

    Article • Journal of Computational Chemistry, January 2009, Wiley

    Dr Takeshi Ishikawa

  68. Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations

    Article • Chemical Physics Letters, January 2009, Elsevier

    Dr Takeshi Ishikawa

  69. Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information Transmission

    Article • The Journal of Physical Chemistry, September 2008, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  70. An application of fragment interaction analysis based on local MP2

    Article • Chemical Physics Letters, September 2008, Elsevier

    Dr Takeshi Ishikawa

  71. How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion

    Article • Journal of the American Chemical Society, February 2008, American Chemical Society (ACS)

    Dr Takeshi Ishikawa

  72. Theoretical study on the structure of the ground state and photo-induced metastable states of [M(CN)5NO]2− (M = Ru, Fe), and mechanism of the photo-rearrangement among them

    Article • Zeitschrift für Kristallographie - Crystalline Materials, January 2008, De Gruyter

    Dr Takeshi Ishikawa

  73. Multi-reference calculations of nitric oxide dimer

    Article • Chemical Physics Letters, January 2008, Elsevier

    Dr Takeshi Ishikawa

  74. Application of the fragment molecular orbital method for determination of atomic charges on polypeptides

    Article • Chemical Physics Letters, December 2007, Elsevier

    Dr Takeshi Ishikawa

  75. Fragment interaction analysis based on local MP2

    Article • Theoretical Chemistry Accounts, July 2007, Springer Science + Business Media

    Dr Takeshi Ishikawa

  76. A fully quantum mechanical simulation study on the lowest n–π∗ state of hydrated formaldehyde

    Article • Chemical Physics Letters, March 2007, Elsevier

    Dr Takeshi Ishikawa

  77. Fragment molecular orbital calculations on red fluorescent protein (DsRed)

    Article • Chemical Physics Letters, January 2007, Elsevier

    Dr Takeshi Ishikawa

  78. Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

    Article • Theoretical Chemistry Accounts, November 2006, Springer Science + Business Media

    Dr Takeshi Ishikawa

  79. A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs

    Article • Theoretical Chemistry Accounts, October 2006, Springer Science + Business Media

    Dr Takeshi Ishikawa

  80. Application of fragment molecular orbital scheme to silicon-containing systems

    Article • Chemical Physics Letters, October 2006, Elsevier

    Dr Takeshi Ishikawa

  81. Fragment molecular orbital calculations on large scale systems containing heavy metal atom

    Article • Chemical Physics Letters, August 2006, Elsevier

    Dr Takeshi Ishikawa

  82. Dynamic polarizability calculation with fragment molecular orbital scheme

    Article • Chemical Physics Letters, February 2006, Elsevier

    Dr Takeshi Ishikawa

  83. Electronic structures and the stabilities of metastable states in [Ru(CN)5NO]2−: A theoretical study

    Article • Chemical Physics Letters, August 2005, Elsevier

    Dr Takeshi Ishikawa

  84. Response to “Comment on ‘Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2−” [J. Chem. Phys. 122, 074314 (2005)]

    Article • The Journal of Chemical Physics, July 2005, American Institute of Physics

    Dr Takeshi Ishikawa

  85. Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2−

    Article • The Journal of Chemical Physics, February 2005, American Institute of Physics

    Dr Takeshi Ishikawa

  86. Theoretical study of lower electronic excitation spectra of [(Re6S8)Cl6]3−

    Article • Chemical Physics Letters, September 2004, Elsevier

    Dr Takeshi Ishikawa

  87. Theoretical study on the photoisomerization of azobenzene

    Article • The Journal of Chemical Physics, October 2001, American Institute of Physics

    Dr Takeshi Ishikawa

  88. Spin Polarized MetastableHe*(23S,1s2s)Stimulated Desorption ofH+Ions

    Article • Physical Review Letters, April 2001, American Physical Society (APS)

    Dr Takeshi Ishikawa