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Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation: A Comparison of Calculation Methods
https://doi.org/10.24517/00011974
https://doi.org/10.24517/00011974e2c77423-3f00-462d-9fae-09c31823dc95
名前 / ファイル | ライセンス | アクション |
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ISCS2013Proceedings-71-78.pdf (650.9 kB)
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Item type | 報告書 / Research Paper(1) | |||||
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公開日 | 2017-10-03 | |||||
タイトル | ||||||
タイトル | Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation: A Comparison of Calculation Methods | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_18ws | |||||
資源タイプ | research report | |||||
ID登録 | ||||||
ID登録 | 10.24517/00011974 | |||||
ID登録タイプ | JaLC | |||||
著者別表示 |
齋藤, 大明
× 齋藤, 大明× 川口, 一朋× 長尾, 秀実 |
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書誌情報 |
Recent development in computational science : Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan 巻 4, p. 71-78, 発行日 2013-02-01 |
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ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 2223-0785 | |||||
出版者 | ||||||
出版者 | Kanazawa e-Publishing | |||||
抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | Accurate methods of computing the affinity of ligand with protein target are strongly needed in the drug discovery process. 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. | |||||
権利 | ||||||
権利情報 | Organizing Committee of ISCS 2013 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |