A hybrid extended ensemble simulation study on the folding process of proteins
| Project/Area Number |
24570189
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Kinki University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
KIKUGAWA Gouta 東北大学, 講師 (90435644)
FUJISAWA Masao 近畿大学, 生物理工学部, 教授 (20258065)
YOSHIDA Hisashi 近畿大学, 生物理工学部, 教授 (50278735)
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| Co-Investigator(Renkei-kenkyūsha) |
TACHIBANA Hideki 近畿大学, 生物理工学部, 教授 (70126118)
AKASAKA Kazuyuki 近畿大学, 先端技術総合研究所, 客員教授 (50025368)
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| Project Period (FY) |
2012-04-01 – 2015-03-31
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| Project Status |
Completed (Fiscal Year 2014)
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| Budget Amount *help |
¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
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| Keywords | 蛋白質 / 分子シミュレーション / 拡張アンサンブル法 / 蛋白質構造 / 反応座標 / 構造空間探索 / 蛋白質フォールディング / フォールディング / 分子動力学シミュレーション |
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| Outline of Final Research Achievements |
We have applied our extended ensemble simulation, MCMD-METAD hybrid method to the several typical issues of protein simulations. Our method has a remarkable advantages against old similar methods, providing clear convergence property. We implemented the method to our molecular dynamics simulation program. Moreover, we then developed a novel long-range potential which significantly accelerates simulations. We implemented it to our simulation program, evaluating properties of several bio-systems. As a results, we found that the search ability of taboo like method, such as METAD, is strongly depend on the pre-determined reaction coordinate. This suggests the good reaction coordinate determination is of paramount importance for protein simulation studies.
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Report
(4 results)
Research Products
(11 results)
