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Amino-acid-dependent main-chain torsion-energy terms for protein systems
http://hdl.handle.net/2237/00029128
http://hdl.handle.net/2237/00029128c7456c7c-8ad8-46b7-bc35-c820e5c5d11a
名前 / ファイル | ライセンス | アクション |
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1_4774159 (1.6 MB)
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2018-12-21 | |||||
タイトル | ||||||
タイトル | Amino-acid-dependent main-chain torsion-energy terms for protein systems | |||||
言語 | en | |||||
著者 |
Sakae, Yoshitake
× Sakae, Yoshitake× Okamoto, Yuko |
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アクセス権 | ||||||
アクセス権 | open access | |||||
アクセス権URI | http://purl.org/coar/access_right/c_abf2 | |||||
権利 | ||||||
言語 | en | |||||
権利情報 | Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.138, n.6, 2013, p.064103) and may be found at (http://dx.doi.org/10.1063/1.4774159). | |||||
抄録 | ||||||
内容記述 | Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters for main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for ψ (N-C^α-C-N) and ζ (C^β-C^α-C-N) angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of α-helical and β-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field. | |||||
言語 | en | |||||
内容記述タイプ | Abstract | |||||
出版者 | ||||||
言語 | en | |||||
出版者 | AIP Publishing | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプresource | http://purl.org/coar/resource_type/c_6501 | |||||
タイプ | journal article | |||||
出版タイプ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||
DOI | ||||||
関連タイプ | isVersionOf | |||||
識別子タイプ | DOI | |||||
関連識別子 | https://doi.org/10.1063/1.4774159 | |||||
ISSN(print) | ||||||
収録物識別子タイプ | PISSN | |||||
収録物識別子 | 0021-9606 | |||||
書誌情報 |
en : The Journal of Chemical Physics 巻 138, 号 6, p. 064103, 発行日 2013-02-14 |
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著者版フラグ | ||||||
値 | publisher |