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- Daniel J. Sindhikara, Fumio Hirata
- The journal of physical chemistry. B
- 2013

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without eitherâ€¦ (More)

- Takashi Imai, Yuichi Harano, Masahiro Kinoshita, Andriy Kovalenko, Fumio Hirata
- The Journal of chemical physics
- 2006

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recentlyâ€¦ (More)

- Andriy Kovalenko, Seiichiro L. Ten-no, Fumio Hirata
- Journal of Computational Chemistry
- 1999

We proposed a modified procedure of the direct inversion in the Å½ . iterative subspace DIIS method to accelerate convergence in the integral equation theory of liquids. We update the DIIS basisâ€¦ (More)

- Takashi Imai, Andriy Kovalenko, Fumio Hirata
- The journal of physical chemistry. B
- 2005

The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of someâ€¦ (More)

- Norio Yoshida, Fumio Hirata
- Journal of Computational Chemistry
- 2006

The three-dimensional reference interaction site model integral equation theory (3D-RISM) combined with the ab initio molecular orbital method (3D-RISM-SCF) is applied to a solvated macromolecularâ€¦ (More)

- Takashi Imai, Naoyuki Miyashita, Yuji Sugita, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
- The journal of physical chemistry. B
- 2011

AcrB is a membrane protein and a multidrug efflux transporter. Although the recently solved X-ray crystal structures of AcrB provide a rough sketch of how drugs efflux, the pathway and mechanism haveâ€¦ (More)

- Takashi Imai, Takahiro Takekiyo, Andriy Kovalenko, Fumio Hirata, Minoru Kato, Yoshihiro Taniguchi
- Biopolymers
- 2005

The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine-rich peptide AK16 from the alpha-helix structure to various random coil structures areâ€¦ (More)

- Yutaka Maruyama, Taku Matsushita, Ryuichi Ueoka, Fumio Hirata
- The journal of physical chemistry. B
- 2011

The free energy and the solvation structures of the G-quadruplex telomeric DNA in pure water and in the 0.1 M aqueous solutions of sodium and potassium chlorides are calculated on the basis of theâ€¦ (More)

Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (a-helical decaglycine) in vacuo, a proteinâ€¦ (More)

- Norio Yoshida, Ryosuke Ishizuka, Hirofumi Sato, Fumio Hirata
- The journal of physical chemistry. B
- 2006

The temperature and density dependence of the molecular and thermodynamic properties of water is investigated theoretically by means of the ab initio electronic structure theory combined with theâ€¦ (More)