Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity
文献类型：期刊论文
| 作者 | Yan ZQ ; Wang J |
| 刊名 | plos one
 |
| 出版日期 | 2013 |
| 卷号 | 8期号:9页码:文献号: e74443 |
| 关键词 | KNOWLEDGE-BASED POTENTIALS COMPUTATIONAL REDESIGN DOCKING BENCHMARK MEAN FORCE MOLECULAR RECOGNITION BINDING-AFFINITY DNA INTERACTIONS ENERGY FUNCTION LIGAND-BINDING DATA-BANK |
| ISSN号 | 1932-6203 |
| 通讯作者 | wang j |
| 中文摘要 | protein-nucleic acid (protein-dna and protein-rna) recognition is fundamental to the regulation of gene expression. determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. however, the progress of protein-nucleic acid structure prediction, especially protein-rna, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. in this work, we developed an accurate scoring function (named as spa-pn, specificity and affinity of the protein-nucleic acid interactions) for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. we applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. in addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of spa-pn. the testing results and comparisons with other scoring functions validated that spa-pn performs well on both the prediction of binding affinity and identification of native conformation. in terms of its performance, spa-pn can be widely used to predict the protein-nucleic acid structures and quantify their interactions. |
| 收录类别 | SCI收录期刊论文 |
| 语种 | 英语 |
| WOS记录号 | WOS:000325423500022 |
| 公开日期 | 2014-04-15 |
| 源URL | [http://ir.ciac.jl.cn/handle/322003/49592]  |
| 专题 | 长春应用化学研究所_长春应用化学研究所知识产出_期刊论文 |
| 推荐引用方式 GB/T 7714 | Yan ZQ,Wang J. Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity[J]. plos one,2013,8(9):文献号: e74443. |
| APA | Yan ZQ,&Wang J.(2013).Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity.plos one,8(9),文献号: e74443. |
| MLA | Yan ZQ,et al."Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity".plos one 8.9(2013):文献号: e74443. |
入库方式： OAI收割
来源：长春应用化学研究所
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