A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions
文献类型：期刊论文
| 作者 | Liu, Yingtao; Xu, Zhijian ; Yang, Zhuo; Chen, Kaixian; Zhu, Weiliang
|
| 刊名 | JOURNAL OF MOLECULAR MODELING
 |
| 出版日期 | 2013-11 |
| 卷号 | 19期号:11页码:5015-5030 |
| 关键词 | Halogen bonding Knowledge-based scoring function Potential of mean forces Protein-ligand interaction sigma-hole |
| ISSN号 | 1610-2940 |
| DOI | 10.1007/s00894-013-2005-7 |
| 文献子类 | Article |
| 英文摘要 | Halogen bonding, a non-covalent interaction between the halogen sigma-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of "docking power", "ranking power" and "scoring power". Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization. |
| WOS关键词 | MECHANICAL METHOD PM6-DH2X ; RATIONAL DRUG DESIGN ; BINDING AFFINITIES ; FORCE-FIELD ; MOLECULAR DOCKING ; SIGMA-HOLE ; GENETIC ALGORITHM ; ACCURATE DOCKING ; PDBBIND DATABASE ; COMPLEXES |
| 资助项目 | National Natural Science Foundation of China[81273435] ; National Natural Science Foundation of China[21021063] ; National Natural Science Foundation of China[91013008] ; State Key Laboratory of Drug Research[SIMM1203KF-01] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000326193200040 |
| 出版者 | SPRINGER |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/277406]  |
| 专题 | 药物发现与设计中心 |
| 通讯作者 | Zhu, Weiliang |
| 作者单位 | Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Struct & Funct, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Yingtao,Xu, Zhijian,Yang, Zhuo,et al. A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions[J]. JOURNAL OF MOLECULAR MODELING,2013,19(11):5015-5030. |
| APA | Liu, Yingtao,Xu, Zhijian,Yang, Zhuo,Chen, Kaixian,&Zhu, Weiliang.(2013).A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions.JOURNAL OF MOLECULAR MODELING,19(11),5015-5030. |
| MLA | Liu, Yingtao,et al."A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions".JOURNAL OF MOLECULAR MODELING 19.11(2013):5015-5030. |
入库方式： OAI收割
来源：上海药物研究所
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