Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features
文献类型：期刊论文
| 作者 | Zhang, YN; Yu, DJ; Li, SS; Fan, YX; Huang, Y; Shen, HB |
| 刊名 | BMC BIOINFORMATICS
 |
| 出版日期 | 2012 |
| 卷号 | 13期号:0 |
| 英文摘要 | Background: Adenosine-5'-triphosphate (ATP) is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex. Results: In this paper, we propose a novel framework for predicting the proteins' functional residues, through which they can bind with ATP molecules. The new prediction protocol is achieved by combination of sequence evolutional information and bi-profile sampling of multi-view sequential features and the sequence derived structural features. The hypothesis for this strategy is single-view feature can only represent partial target's knowledge and multiple sources of descriptors can be complementary. Conclusions: Prediction performances evaluated by both 5-fold and leave-one-out jackknife cross-validation tests on two benchmark datasets consisting of 168 and 227 non-homologous ATP binding proteins respectively demonstrate the efficacy of the proposed protocol. Our experimental results also reveal that the residue structural characteristics of real protein-ATP binding sites are significant different from those normal ones, for example the binding residues do not show high solvent accessibility propensities, and the bindings prefer to occur at the conjoint points between different secondary structure segments. Furthermore, results also show that performance is affected by the imbalanced training datasets by testing multiple ratios between positive and negative samples in the experiments. Increasing the dataset scale is also demonstrated useful for improving the prediction performances. |
| WOS记录号 | WOS:000313260800001 |
| 公开日期 | 2013-03-18 |
| 源URL | [http://202.127.1.142/handle/181331/7045]  |
| 专题 | 上海技术物理研究所_上海技物所 |
| 推荐引用方式 GB/T 7714 | Zhang, YN,Yu, DJ,Li, SS,et al. Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features[J]. BMC BIOINFORMATICS,2012,13(0). |
| APA | Zhang, YN,Yu, DJ,Li, SS,Fan, YX,Huang, Y,&Shen, HB.(2012).Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.BMC BIOINFORMATICS,13(0). |
| MLA | Zhang, YN,et al."Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features".BMC BIOINFORMATICS 13.0(2012). |
入库方式： OAI收割
来源：上海技术物理研究所
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