Development of new molecular dynamics simulation methods and application to protein folding problem
| Project/Area Number |
23740325
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Biophysics/Chemical physics
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| Research Institution | Okazaki Research Facilities, National Institutes of Natural Sciences |
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Principal Investigator |
OKUMURA HISASHI 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授 (80360337)
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| Project Period (FY) |
2011-04-28 – 2015-03-31
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| Project Status |
Completed (Fiscal Year 2014)
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| Budget Amount *help |
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
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| Keywords | 分子動力学 / タンパク質 / ペプチド / 分子動力学法 / シミュレーション |
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| Outline of Final Research Achievements |
Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics simulations tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is the replica-exchange method.
We proposed a new type of the replica-exchange method, which is referred to as helix-strand replica-exchange molecular dynamics method. In this method umbrella potential which enhances alpha-helix or beta-strand conformation is exchanged. We applied this method to a design peptide and compared the results with those obtained by usual replica-exchange method.
We also proposed a better alternative to the replica-exchange method, which we refer to as the replica-permutation method. In replica-permutation method, not only exchanges between two replicas but also permutations among more than two replicas are performed.
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Report
(5 results)
Research Products
(43 results)
