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Towards Fragment-Based Drug Design Using a New Ligand Mapping Method Based on Molecular Liquid Theory: Application to FK506-Binding Protein
Takashi Imai, Yutaka Maruyama, Fumio Hirata, Yuji Sugita
Submitted for publication
Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway
Takashi Imai, Naoyuki Miyashita, Yuji Sugita, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
The Journal of Physical Chemistry B, 115 (25), 8288–8295 (June 30, 2011)
Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation
Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita
Journal of Computational Chemistry, 32 (2), 260–270 (January 30, 2011)
Visualizing Water Molecule Distribution by Atomic Force Microscopy
Kenjiro Kimura, Shinichiro Ido, Noriaki Oyabu, Kei Kobayashi, Yoshiki Hirata, Takashi Imai, Hirofumi Yamada
The Journal of Chemical Physics, 132 (19), 194705-(1–5) (May 21, 2010)
Dynamic Correlation between Pressure-Induced Protein Structural Transition and Water Penetration
Takashi Imai, Yuji Sugita
The Journal of Physical Chemistry B, 114 (6), 2281–2286 (February 18, 2010)
Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design
Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
Journal of the American Chemical Society, 131 (34), 12430–12440 (September 2, 2009)
Molecular Thermodynamics of Trifluoroethanol-Induced Helix Formation: Analysis of the Solvation Structure and Free Energy by the 3D-RISM Theory
Takashi Imai, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
Interdisciplinary Sciences: Computational Life Sciences, 1 (2), 156–160 (June 2009)
Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory
Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata
Journal of the American Chemical Society, 131 (11), 3852–3853 (March 25, 2009)
A Highly Parallelizable Integral Equation Theory for Three Dimensional Solvent Distribution Function: Application to Biomolecules
Daisuke Yokogawa, Hirofumi Sato, Takashi Imai, Shigeyoshi Sakaki
The Journal of Chemical Physics, 130 (6), 064111-(1–6) (February 14, 2009)
Uncovering the Physical Origin of the Difference between Aliphatic Chain and Aromatic Ring in the “Hydrophobic” Effects on Partial Molar Volume
Takashi Imai, Yu Hisadomi, Seiji Sawamura, Yoshihiro Taniguchi
The Journal of Chemical Physics, 128 (4), 044502-(1–6) (January 28, 2008)
Three-Dimensional Distribution Function Theory for the Prediction of Protein-Ligand Binding Sites and Affinities: Application to the Binding of Noble Gases to Hen Egg-White Lysozyme in Aqueous Solution
Takashi Imai, Ryusuke Hiraoka, Tomoyoshi Seto, Andriy Kovalenko, Fumio Hirata
The Journal of Physical Chemistry B, 111 (39), 11585–11591 (October 4, 2007)
Theoretical Study of the Partial Molar Volume Change Associated with the Pressure-Induced Structural Transition of Ubiquitin
Takashi Imai, Shusaku Ohyama, Andriy Kovalenko, Fumio Hirata
Protein Science, 16 (9), 1927–1933 (September 2007)
Theoretical Analysis on Changes in Thermodynamic Quantities upon Protein Folding: Essential Role of Hydration
Takashi Imai, Yuichi Harano, Masahiro Kinoshita, Andriy Kovalenko, Fumio Hirata
The Journal of Chemical Physics, 126 (22), 225102-(1–9) (June 14, 2007)
Locating Missing Water Molecules in Protein Cavities by the Three-Dimensional Reference Interaction Site Model Theory of Molecular Solvation
Takashi Imai, Ryusuke Hiraoka, Andriy Kovalenko, Fumio Hirata
Proteins: Structure, Function, and Bioinformatics, 66 (4), 804–813 (March 1, 2007)
Theoretical Study of the Cosolvent Effect on the Partial Molar Volume Change of Staphylococcal Nuclease Associated with Pressure Denaturation
Takeshi Yamazaki, Takashi Imai, Fumio Hirata, Andriy Kovalenko
The Journal of Physical Chemistry B, 111 (5), 1206–1212 (February 8, 2007)
Selective Ion-Binding by Protein Probed with the 3D-RISM Theory
Norio Yoshida, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai, Fumio Hirata
Journal of the American Chemical Society, 128 (37), 12042–12043 (September 20, 2006)
A Theoretical Analysis on Hydration Thermodynamics of Proteins
Takashi Imai, Yuichi Harano, Masahiro Kinoshita, Andriy Kovalenko, Fumio Hirata
The Journal of Chemical Physics, 125 (2), 024911-(1–7) (July 14, 2006)
Theoretical Study of Volume Changes Accompanying Xenon-Lysozyme Binding: Implications for the Molecular Mechanism of Pressure Reversal of Anesthesia
Takashi Imai, Hideto Isogai, Tomoyoshi Seto, Andriy Kovalenko, Fumio Hirata
The Journal of Physical Chemistry B, 110 (24), 12149–12154 (June 22, 2006)
Water Molecules in a Protein Cavity Detected by a Statistical-Mechanical Theory
Takashi Imai, Ryusuke Hiraoka, Andriy Kovalenko, Fumio Hirata
Journal of the American Chemical Society, 127 (44), 15334–15335 (November 9, 2005)
Reply to “Comment on ‘Hydrophobic Effects on Partial Molar Volume’”
Takashi Imai, Fumio Hirata
The Journal of Chemical Physics, 123 (16), 167104-(1–2) (October 22, 2005)
Theoretical Study of Volume Changes Associated with the Helix-Coil Transition of an Alanine-Rich Peptide in Aqueous Solution
Takashi Imai, Takahiro Takekiyo, Andriy Kovalenko, Fumio Hirata, Minoru Kato, Yoshihiro Taniguchi
Biopolymers, 79 (2), 97–105 (October 5, 2005)
Partial Molar Volume of Proteins Studied by the Three-Dimensional Reference Interaction Site Model Theory
Takashi Imai, Andriy Kovalenko, Fumio Hirata
The Journal of Physical Chemistry B, 109 (14), 6658–6665 (April 14, 2005)
[Special issue “David Chandler Festschrift”]
Hydrophobic Effects on Partial Molar Volume
Takashi Imai, Fumio Hirata
The Journal of Chemical Physics, 122 (9), 094509-(1–6) (March 1, 2005)
Solvation Thermodynamics of Protein Studied by the 3D-RISM Theory
Takashi Imai, Andriy Kovalenko, Fumio Hirata
Chemical Physics Letters, 395 (1–3), 1–6 (September 1, 2004)
Statistical Sequence Analyses of G-Protein-Coupled Receptors: Structural and Functional Characteristics Viewed with Periodicities of Entropy, Hydrophobicity, and Volume
Takashi Imai, Norihisa Fujita
Proteins: Structure, Function, and Bioinformatics, 56 (4), 650–660 (September 1, 2004)
Detection of Pairwise Residue Proximity by Covariation Analysis for 3D-Structure Prediction of G-Protein-Coupled Receptors
Wataru Nemoto, Takashi Imai, Takuya Takahashi, Takeshi Kikuchi, Norihisa Fujita
The Protein Journal, 23 (6), 427–435 (August 2004)
Temperature and Pressure Effects on Conformational Equilibria of Alanine Dipeptide in Aqueous Solution
Takahiro Takekiyo, Takashi Imai, Minoru Kato, Yoshihiro Taniguchi
Biopolymers, 73 (2), 283–290 (February 5, 2004)
Partial Molar Volume and Compressibility of a Molecule with Internal Degrees of Freedom
Takashi Imai, Fumio Hirata
The Journal of Chemical Physics, 119 (11), 5623–5631 (September 15, 2003)
Partial Molar Volume and Compressibility of Alkali-Halide Ions in Aqueous Solution: Hydration Shell Analysis with an Integral Equation Theory of Molecular Liquids
Takashi Imai, Hiroyasu Nomura, Masahiro Kinoshita, Fumio Hirata
The Journal of Physical Chemistry B, 106 (29), 7308–7314 (July 25, 2002)
Theoretical Study for Volume Changes Associated with the Helix-Coil Transition of Peptides
Takashi Imai, Yuichi Harano, Andriy Kovalenko, Fumio Hirata
Biopolymers, 59 (7), 512–519 (December 2001)
Improvement of the Reference Interaction Site Model Theory for Calculating the Partial Molar Volume of Amino Acids and Polypeptides
Masahiro Kinoshita, Takashi Imai, Andriy Kovalenko, Fumio Hirata
Chemical Physics Letters, 348 (3–4), 337–342 (November 9, 2001)
Integral Equations for Molecular Fluids Based on Interaction Site Model: Density-Functional Formulation
Tomonari Sumi, Takashi Imai, Fumio Hirata
The Journal of Chemical Physics, 115 (14), 6653–6662 (October 8, 2001)
Theoretical Study for Partial Molar Volume of Amino Acids and Polypeptides by the Three-Dimensional Reference Interaction Site Model
Yuichi Harano, Takashi Imai, Andriy Kovalenko, Masahiro Kinoshita, Fumio Hirata
The Journal of Chemical Physics, 114 (21), 9506–9511 (June 1, 2001)
Theoretical Study for Partial Molar Volume of Amino Acids in Aqueous Solution: Implication of Ideal Fluctuation Volume
Takashi Imai, Masahiro Kinoshita, Fumio Hirata
The Journal of Chemical Physics, 112 (21), 9469–9478 (June 1, 2000)
Salt Effect on Stability and Solvation Structure of Peptide: An Integral Equation Study
Takashi Imai, Masahiro Kinoshita, Fumio Hirata
Bulletin of Chemical Society of Japan, 73 (5), 1113–1122 (May 2000)