Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials
文献类型：期刊论文
| 作者 | Zhang, Dinglin; Wang, Honglei; Li, Guohui; Shen, Hujun; Li, Yan |
| 刊名 | JOURNAL OF CHEMICAL THEORY AND COMPUTATION
 |
| 出版日期 | 2016-02-01 |
| 卷号 | 12期号:2页码:676-693 |
| ISSN号 | 1549-9618 |
| DOI | 10.1021/acs.jctc.5b00903 |
| 文献子类 | Article |
| 英文摘要 | In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. |
| WOS关键词 | MOLECULAR-DYNAMICS SIMULATIONS ; PACE FORCE-FIELD ; STRUCTURAL BASIS ; BASE-PAIRS ; DNA ; RNA ; PROTEINS ; COMPLEX ; WOBBLE ; DUPLEX |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| WOS记录号 | WOS:000370112900021 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://cas-ir.dicp.ac.cn/handle/321008/171254]  |
| 专题 | 大连化学物理研究所_中国科学院大连化学物理研究所 |
| 通讯作者 | Li, Guohui |
| 作者单位 | Chinese Acad Sci, Dalian Inst Chem Phys, Lab Mol Modeling & Design, State Key Lab Mol React Dynam, Dalian 116023, Liaoning Provin, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Dinglin,Wang, Honglei,Li, Guohui,et al. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2016,12(2):676-693. |
| APA | Zhang, Dinglin,Wang, Honglei,Li, Guohui,Shen, Hujun,&Li, Yan.(2016).Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,12(2),676-693. |
| MLA | Zhang, Dinglin,et al."Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12.2(2016):676-693. |
入库方式： OAI收割
来源：大连化学物理研究所
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