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Exhaustive sampling of intrinsically disordered protein docking conformation with ALSD simulation
https://repo.qst.go.jp/records/86119
https://repo.qst.go.jp/records/86119d284af0a-6d70-4649-9d3f-f9fb960344b7
| Item type | 学術雑誌論文 / Journal Article(1) | |||||
|---|---|---|---|---|---|---|
| 公開日 | 2021-07-06 | |||||
| タイトル | ||||||
| タイトル | Exhaustive sampling of intrinsically disordered protein docking conformation with ALSD simulation | |||||
| 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_6501 | |||||
| 資源タイプ | journal article | |||||
| アクセス権 | ||||||
| アクセス権 | metadata only access | |||||
| アクセス権URI | http://purl.org/coar/access_right/c_14cb | |||||
| 著者 |
Jinzen, Ikebe
× Jinzen, Ikebe× Hidetoshi, Kono× Hidetoshi, Kono |
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| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | We tried to predict docking structures of a complex system of an intrinsically disordered protein (IDP) with high structural flexibility and the receptor protein using Adaptive Lambda Square Dynamics (ALSD) method, which is a molecular dynamics (MD) simulation to efficiently search conformations of biomolecules. Conventionally, since docking pose search calculations mostly treat conformations of proteins and the substrates as rigid bodies, it is difficult to apply these methods to IDPs, which do not have specific conformations. In this study, we considered conformational changes of proteins and substrates and performed an exhaustive conformational search for their docking poses. Because the conformational degrees of freedom of this system are much larger than those of systems to which ALSD has been successfully applied so far, the docking structure observed in the NMR models could not be reproduced within the project period. However, this study could clarify a specific problem occurring in conformation sampling of a system with high degrees of freedom and suggested a direction to improve ALSD. | |||||
| 書誌情報 |
平成２９年度 HPCI 利用研究成果集 発行日 2022-05 |
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| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | https://www.hpci-office.jp/annex/resrep/?p=1996 | |||||
