Selected Paper : A Fast Convergent Simulated Annealing Algorithm for Protein-Folding : Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method
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<jats:title>Abstract</jats:title> <jats:p>A Simulated Annealing (SA) algorithm is combined with our recently developed conformational search technique, Outlier FLOODding (OFLOOD) method [J. Comput. Chem. 2015, 36, 97], to avoid a slow convergence in finding a global minimum by the conventional SA (CSA). This method is referred to as SA-OFLOOD and designed for an efficient SA algorithm that robustly detects global minimum states in the protein-folding problems. As a demonstration, SA-OFLOOD was applied to reproduce the folding process of Trp-cage from a fully extended to the native states in implicit solvent. Through the demonstration, SA-OFLOOD successfully predicted the native state of Trp-cage within errors of 0.6 ± 0.2 Å Cα root mean square deviation (RMSD) with only 200 ns simulation time. In contrast, both CSA with sufficiently slow temperature scheduling and canonical MD simulations at room temperature (300 K) failed to find the native state (more than 3.0 Å Cα RMSD), indicating the strength of SA-OFLOOD on the protein-folding problem. As an application to a realistic system, SA-OFLOOD was applied to the folding of Trp-cage in explicit solvent, and the native state was also sampled within Cα RMSD of 1.0 Å through a nanosecond-order simulation time.</jats:p>
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- Bulletin of the Chemical Society of Japan
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Bulletin of the Chemical Society of Japan 89 (11), 1361-1367, 2016-11
Tokyo : Chemical Society of Japan
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詳細情報 詳細情報について
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- CRID
- 1524232504496045952
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- NII論文ID
- 130005316155
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- NII書誌ID
- AA00580132
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- ISSN
- 00092673
- 13480634
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- NDL書誌ID
- 027719460
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- 本文言語コード
- en
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- NDL 雑誌分類
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- ZP1(科学技術--化学・化学工業)
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- データソース種別
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- NDL
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