Institute of Computing Technology, Chinese Academy IR
| COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization | |
| Reza, Md Selim1,2; Zhang, Huiling1,2; Hossain, Md Tofazzal1,2; Jin, Langxi3; Feng, Shengzhong2; Wei, Yanjie1,2 | |
| 2021-07-01 | |
| 发表期刊 | MEMBRANES
 |
| 卷号 | 11期号:7页码:21 |
| 摘要 | Protein contact prediction helps reconstruct the tertiary structure that greatly determines a protein's function; therefore, contact prediction from the sequence is an important problem. Recently there has been exciting progress on this problem, but many of the existing methods are still low quality of prediction accuracy. In this paper, we present a new mixed integer linear programming (MILP)-based consensus method: a Consensus scheme based On a Mixed integer linear opTimization method for prOtein contact Prediction (COMTOP). The MILP-based consensus method combines the strengths of seven selected protein contact prediction methods, including CCMpred, EVfold, DeepCov, NNcon, PconsC4, plmDCA, and PSICOV, by optimizing the number of correctly predicted contacts and achieving a better prediction accuracy. The proposed hybrid protein residue-residue contact prediction scheme was tested in four independent test sets. For 239 highly non-redundant proteins, the method showed a prediction accuracy of 59.68%, 70.79%, 78.86%, 89.04%, 94.51%, and 97.35% for top-5L, top-3L, top-2L, top-L, top-L/2, and top-L/5 contacts, respectively. When tested on the CASP13 and CASP14 test sets, the proposed method obtained accuracies of 75.91% and 77.49% for top-L/5 predictions, respectively. COMTOP was further tested on 57 non-redundant alpha-helical transmembrane proteins and achieved prediction accuracies of 64.34% and 73.91% for top-L/2 and top-L/5 predictions, respectively. For all test datasets, the improvement of COMTOP in accuracy over the seven individual methods increased with the increasing number of predicted contacts. For example, COMTOP performed much better for large number of contact predictions (such as top-5L and top-3L) than for small number of contact predictions such as top-L/2 and top-L/5. The results and analysis demonstrate that COMTOP can significantly improve the performance of the individual methods; therefore, COMTOP is more robust against different types of test sets. COMTOP also showed better/comparable predictions when compared with the state-of-the-art predictors. |
| 关键词 | protein residue-residue contact contact prediction mixed integer linear programming machine learning protein sequence |
| DOI | 10.3390/membranes11070503 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | National Key Research and Development Program of China[2018YFB0204403] ; Strategic Priority CAS Project[XDB38000000] ; National Science Foundation of China[U1813203] ; Shenzhen Basic Research Fund[JCYJ20200109114818703] ; Shenzhen Basic Research Fund[RCYX2020071411473419] ; Shenzhen Basic Research Fund[JSGG20201102163800001] ; CAS Key Lab[2011DP173015] ; Youth Innovation Promotion Association, CAS ; Outstanding Youth Innovation Fund (CAS-SIAT) |
| WOS研究方向 | Biochemistry & Molecular Biology ; Chemistry ; Engineering ; Materials Science ; Polymer Science |
| WOS类目 | Biochemistry & Molecular Biology ; Chemistry, Physical ; Engineering, Chemical ; Materials Science, Multidisciplinary ; Polymer Science |
| WOS记录号 | WOS:000676905300001 |
| 出版者 | MDPI |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://119.78.100.204/handle/2XEOYT63/17444 |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Wei, Yanjie |
| 作者单位 | 1.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Ctr High Performance Comp, Joint Engn Res Ctr Hlth Big Data Intelligent Anal, Shenzhen Inst Adv Technol, Shenzhen 518055, Peoples R China 3.Harbin Univ Sci & Technol, Sch Comp Sci & Technol, Dept Comp Sci & Technol, 52 Xuefu Rd, Harbin 150080, Peoples R China |
| 推荐引用方式 GB/T 7714 | Reza, Md Selim,Zhang, Huiling,Hossain, Md Tofazzal,et al. COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization[J]. MEMBRANES,2021,11(7):21. |
| APA | Reza, Md Selim,Zhang, Huiling,Hossain, Md Tofazzal,Jin, Langxi,Feng, Shengzhong,&Wei, Yanjie.(2021).COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization.MEMBRANES,11(7),21. |
| MLA | Reza, Md Selim,et al."COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization".MEMBRANES 11.7(2021):21. |
| 条目包含的文件 | 条目无相关文件。 | |||||
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