Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction
文献类型：期刊论文
| 作者 | de Oliveira, SHP; Law, EC; Shi, JY; Deane, CM |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2018 |
| 卷号 | 34期号:7页码:1132-1140 |
| 关键词 | Secondary Structure Prediction Coevolution Methods Database Stepwise Contact Rosetta Server Algorithm Quality Model |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btx722 |
| 文献子类 | 期刊论文 |
| 英文摘要 | Motivation: Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. Results: We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models ( TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. |
| 语种 | 英语 |
| WOS记录号 | WOS:000428840000008 |
| 源URL | [http://ir.sinap.ac.cn/handle/331007/29130]  |
| 专题 | 上海应用物理研究所_中科院上海应用物理研究所2011-2017年 |
| 作者单位 | 1.de Oliveira, SHP 2.Law, EC 3.Shi, JY 4.Deane, CM |
| 推荐引用方式 GB/T 7714 | de Oliveira, SHP,Law, EC,Shi, JY,et al. Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction[J]. BIOINFORMATICS,2018,34(7):1132-1140. |
| APA | de Oliveira, SHP,Law, EC,Shi, JY,&Deane, CM.(2018).Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.BIOINFORMATICS,34(7),1132-1140. |
| MLA | de Oliveira, SHP,et al."Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction".BIOINFORMATICS 34.7(2018):1132-1140. |
入库方式： OAI收割
来源：上海应用物理研究所
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