※一部利用できない機能があります
| 1.
論文 |
論文
|
Sri, R. Natasia ; Saito, Hiroaki ; Mizukami, Taku ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Solvation free energy has valuable role as represents the desolvation cost of a molecu-lar binding interaction, which is
…
very important in a variety of chemical and biological processes. Therefore, many computational methods have been explored to predict this value. In this study, we attempted to find the correlation between experimental and calculated value of solvation free energy of proteins, containing organic molecules, by using quantitative structure property relation-ship (QSPR) model. To obtained a comparable value of solvation free energy which will be used as reference in QSPR model, we adopted energy representation (ER) method. And as this method works through molecular dynamic (MD) simulation, we then performed the MD simulation prior to the calculation by ER method. The results showed that the predicted solvation free energies were quite close to calculated values by ER method. We also found that the values of solvation free energy, both in MD simulation and ER method, were well correlated to solvent accessible surface area of hydrophobic portion.<br />Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
続きを見る
|
||||
| 2.
論文 |
論文
|
Meidy, Triana Pakpahan ; Saito, Hiroaki ; Kawaguchi, Kazutomo ; Nagao, Hidemi
概要:
Accurate methods of computing the affinity of ligand with protein target are strongly needed in the drug discovery proce
…
ss. Many attempts have been made and several algorithms have been developed for this purpose. We compared the protein-ligand binding free energies (∆G) in various methods include docking score function, combining docking score function and molecular dynamics (MD) simulation with explicit and implicit solvent model, and molecular-mechanics Poisson Boltzmann surface area (MM-PBSA) approach with and without the inclusion of entropic contributions. We tested these various methods to human plasminogen kringle-3 domain protein with the ligand trans-(aminomethyl) cyclohexanecarboxylic acid (AMCHA). The results showed the comparison between these various methods and the experimental affinity value. We found that combining docking score function and MD simulation with explicit solvent model was more favorable and close to the experimental result. This indicated that combining docking score function and MD simulation with explicit solvent model could be more accurate and effective in the protein-ligand binding free energy calculation.
続きを見る
|
||||
| 3.
論文 |
論文
|
Micke, Rusmerryani ; Gia, Septiana ; Kawamoto, Shuhei ; Hiroaki, Saito ; Nishikawa, Kiyoshi ; Nagao, Hidemi
概要:
Due to the soft and flexible structure, lipid molecule forms various shapes such as micelle, bilayer and vesicle. In thes
…
e systems, since the spherical micelle can be applied to the application of drag delivery system, the analysis of detailed structure and dynamics of the micelle is important. In this study, we carried out molecular dynamics (MD) simulations of the spherical micelles dimer in water solvent to investigate the dynamical structure and correlated motion of the micelle dimer. The MD simulations were run under the constant NPT and NVT conditions with periodic boundary. We adopted the ASIC analysis, which is based on the aperture, symme-try, isotropy, and compactness of the micelle structure to analyze the shape fluctuations for each micelle. From this analysis, we show the stability and correlated motion of spherical micelle and investigate the patterns of synchronization motions between micelle dimer. The mutual fluctuations were periodically shown in the constant NVT simulation, implying that the existence of synchro-nization phenomena between micelle dimer.
続きを見る
|
