Improving the quality of 3D-QSAR by using flexible-ligand receptor models
文献类型：期刊论文
| 作者 | Pei, JF; Chen, H; Liu, ZM; Han, XF; Wang, Q; Shen, B; Zhou, JJ; Lai, LH |
| 刊名 | JOURNAL OF CHEMICAL INFORMATION AND MODELING
 |
| 出版日期 | 2005-11-01 |
| 卷号 | 45期号:6页码:1920-1933 |
| 关键词 | gamma-aminobutyric-acid binding free-energy pseudoreceptor models surface models construction inhibitors alignment 4d-qsar qsar representation |
| ISSN号 | 1549-9596 |
| 其他题名 | J. Chem Inf. Model. |
| 中文摘要 | To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to achieve minimal docking energies; (2) the receptor atoms are spatially moveable in the process of genetic evolving in order to avoid improper initial receptor shapes; and (3) void receptor sites are specially favored in order to obtain open receptor models that allow large gaps. Advantages of an open model include less noise information, a smaller risk of overfitting, and ease of locating the key interaction sites. The latter two features, inherited from the previous FLARM 1.0 method, can improve the predictive ability of the 3D-QSAR models, while the first feature is newly implemented to relieve the uncertainty caused by improper conformation and alignment. Three FLARM 2.0 case studies were performed, and the results show that FLARM 2.0 models are highly predictive and robust. FLARM 2.0 pseudoreceptor models can correspond well with the pharmacophore models and/or the binding sites of the real protein receptors. |
| 英文摘要 | To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to achieve minimal docking energies; (2) the receptor atoms are spatially moveable in the process of genetic evolving in order to avoid improper initial receptor shapes; and (3) void receptor sites are specially favored in order to obtain open receptor models that allow large gaps. Advantages of an open model include less noise information, a smaller risk of overfitting, and ease of locating the key interaction sites. The latter two features, inherited from the previous FLARM 1.0 method, can improve the predictive ability of the 3D-QSAR models, while the first feature is newly implemented to relieve the uncertainty caused by improper conformation and alignment. Three FLARM 2.0 case studies were performed, and the results show that FLARM 2.0 models are highly predictive and robust. FLARM 2.0 pseudoreceptor models can correspond well with the pharmacophore models and/or the binding sites of the real protein receptors. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Physical Sciences ; Technology |
| 类目[WOS] | Chemistry, Medicinal ; Chemistry, Multidisciplinary ; Computer Science, Information Systems ; Computer Science, Interdisciplinary Applications |
| 研究领域[WOS] | Pharmacology & Pharmacy ; Chemistry ; Computer Science |
| 关键词[WOS] | GAMMA-AMINOBUTYRIC-ACID ; BINDING FREE-ENERGY ; PSEUDORECEPTOR MODELS ; SURFACE MODELS ; CONSTRUCTION ; INHIBITORS ; ALIGNMENT ; 4D-QSAR ; QSAR ; REPRESENTATION |
| 收录类别 | SCI |
| 原文出处 | |
| 语种 | 英语 |
| WOS记录号 | WOS:000233689400057 |
| 公开日期 | 2013-10-25 |
| 版本 | 出版稿 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/4179]  |
| 专题 | 过程工程研究所_研究所（批量导入） |
| 作者单位 | 1.Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China 2.Peking Univ, State Key Lab Struct Chem Stable & Unstable Speci, Coll Med, Beijing 100871, Peoples R China 3.Peking Univ, Ctr Theoret Biol, Beijing 100871, Peoples R China 4.Chinese Acad Sci, Comp Network Informat Ctr, Beijing 100080, Peoples R China 5.Chinese Acad Sci, Inst Proc Engn, Beijing 100080, Peoples R China |
| 推荐引用方式 GB/T 7714 | Pei, JF,Chen, H,Liu, ZM,et al. Improving the quality of 3D-QSAR by using flexible-ligand receptor models[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2005,45(6):1920-1933. |
| APA | Pei, JF.,Chen, H.,Liu, ZM.,Han, XF.,Wang, Q.,...&Lai, LH.(2005).Improving the quality of 3D-QSAR by using flexible-ligand receptor models.JOURNAL OF CHEMICAL INFORMATION AND MODELING,45(6),1920-1933. |
| MLA | Pei, JF,et al."Improving the quality of 3D-QSAR by using flexible-ligand receptor models".JOURNAL OF CHEMICAL INFORMATION AND MODELING 45.6(2005):1920-1933. |
入库方式： OAI收割
来源：过程工程研究所
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