气候变化领域集成服务门户(CCPortal): Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction

CCPortal

DOI	10.1073/pnas.2110828118
	Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction
	Yang P.; Zheng W.; Ning K.; Zhang Y.
发表日期	2021
ISSN	1091-6490
卷号	118 期号:49
英文摘要	Information derived from metagenome sequences through deep-learning techniques has significantly improved the accuracy of template free protein structure modeling. However, most of the deep learning-based modeling studies are based on blind sequence database searches and suffer from low efficiency in computational resource utilization and model construction, especially when the sequence library becomes prohibitively large. We proposed a MetaSource model built on 4.25 billion microbiome sequences from four major biomes (Gut, Lake, Soil, and Fermentor) to decode the inherent linkage of microbial niches with protein homologous families. Large-scale protein family folding experiments on 8,700 unknown Pfam families showed that a microbiome targeted approach with multiple sequence alignment constructed from individual MetaSource biomes requires more than threefold less computer memory and CPU (central processing unit) time but generates contact-map and three-dimensional structure models with a significantly higher accuracy, compared with that using combined metagenome datasets. These results demonstrate an avenue to bridge the gap between the rapidly increasing metagenome databases and the limited computing resources for efficient genome-wide database mining, which provides a useful bluebook to guide future microbiome sequence database and modeling development for high-accuracy protein structure and function prediction.
英文关键词	deep learning; microbiome; multiple sequence alignments; protein homologous families; protein structure prediction
语种	英语
scopus关键词	protein; algorithm; biology; chemistry; ecosystem; genetics; human; metagenome; microflora; molecular evolution; procedures; protein conformation; protein database; protein folding; sequence alignment; sequence analysis; sequence homology; Algorithms; Computational Biology; Databases, Protein; Deep Learning; Ecosystem; Evolution, Molecular; Humans; Metagenome; Microbiota; Neural Networks, Computer; Protein Conformation; Protein Folding; Proteins; Sequence Alignment; Sequence Analysis, Protein; Sequence Homology
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/250941
作者单位	Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; zhng@umich.edu; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109; ningkang@hust.edu.cn zhng@umich.edu; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, Un...
推荐引用方式 GB/T 7714	Yang P.,Zheng W.,Ning K.,et al. Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction[J],2021,118(49).
APA	Yang P.,Zheng W.,Ning K.,&Zhang Y..(2021).Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.Proceedings of the National Academy of Sciences of the United States of America,118(49).
MLA	Yang P.,et al."Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction".Proceedings of the National Academy of Sciences of the United States of America 118.49(2021).