|
1
|
Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M. An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins. J Chem Phys 2019; 150:175101. [DOI: 10.1063/1.5093110] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Simon Hikiri
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masao Inoue
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
|
2
|
Yildirim A, Wassenaar TA, van der Spoel D. Statistical efficiency of methods for computing free energy of hydration. J Chem Phys 2018; 149:144111. [DOI: 10.1063/1.5041835] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Ahmet Yildirim
- Department of Physics, Siirt University, Siirt 56100, Turkey
| | - Tsjerk A. Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David van der Spoel
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala,
Sweden
| |
Collapse
|
|
3
|
Maruyama Y, Mitsutake A. Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT. J Phys Chem B 2017; 121:9881-9885. [DOI: 10.1021/acs.jpcb.7b08487] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yutaka Maruyama
- Co-Design Team,
FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science, Kobe 650-0047, Japan
| | - Ayori Mitsutake
- Department
of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
|
4
|
Hikiri S, Yoshidome T, Ikeguchi M. Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates. J Chem Theory Comput 2016; 12:5990-6000. [DOI: 10.1021/acs.jctc.6b00563] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Hikiri
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Yoshidome
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| |
Collapse
|
|
5
|
Oshima H, Kinoshita M. A highly efficient hybrid method for calculating the hydration free energy of a protein. J Comput Chem 2015; 37:712-23. [DOI: 10.1002/jcc.24253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
| |
Collapse
|