FALCON2: a web server for high-quality prediction of protein tertiary structures

doi:10.1186/s12859-021-04353-8

	FALCON2: a web server for high-quality prediction of protein tertiary structures
	Kong, Lupeng 1,2; Ju, Fusong 1,2; Zhang, Haicang 1,2; Sun, Shiwei 1,2; Bu, Dongbo 1,2
	2021-09-15
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	22 期号:1 页码:14
摘要	Background Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a template-based modeling approach (called ProALIGN) and an ab initio prediction approach (called ProFOLD). Briefly speaking, ProALIGN aligns a target protein with templates through exploiting the patterns of context-specific alignment motifs and then builds the final structure with reference to the homologous templates. In contrast, ProFOLD uses an end-to-end neural network to estimate inter-residue distances of target proteins and builds structures that satisfy these distance constraints. These two approaches emphasize different characteristics of target proteins: ProALIGN exploits structure information of homologous templates of target proteins while ProFOLD exploits the co-evolutionary information carried by homologous protein sequences. Recent progress has shown that the combination of template-based modeling and ab initio approaches is promising. Results In the study, we present FALCON2, a web server that integrates ProALIGN and ProFOLD to provide high-quality protein structure prediction service. For a target protein, FALCON2 executes ProALIGN and ProFOLD simultaneously to predict possible structures and selects the most likely one as the final prediction result. We evaluated FALCON2 on widely-used benchmarks, including 104 CASP13 (the 13th Critical Assessment of protein Structure Prediction) targets and 91 CASP14 targets. In-depth examination suggests that when high-quality templates are available, ProALIGN is superior to ProFOLD and in other cases, ProFOLD shows better performance. By integrating these two approaches with different emphasis, FALCON2 server outperforms the two individual approaches and also achieves state-of-the-art performance compared with existing approaches. Conclusions By integrating template-based modeling and ab initio approaches, FALCON2 provides an easy-to-use and high-quality protein structure prediction service for the community and we expect it to enable insights into a deep understanding of protein functions.
关键词	Protein structure prediction Template-based modeling Ab initio prediction Protein structure prediction web service
DOI	10.1186/s12859-021-04353-8
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2020YFA0907000] ; National Natural Science Foundation of China[31671369] ; National Natural Science Foundation of China[31770775] ; National Natural Science Foundation of China[62072435]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000696230400001
出版者	BMC
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17203
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu, Dongbo
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Big Data Acad, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Kong, Lupeng,Ju, Fusong,Zhang, Haicang,et al. FALCON2: a web server for high-quality prediction of protein tertiary structures[J]. BMC BIOINFORMATICS,2021,22(1):14.
APA	Kong, Lupeng,Ju, Fusong,Zhang, Haicang,Sun, Shiwei,&Bu, Dongbo.(2021).FALCON2: a web server for high-quality prediction of protein tertiary structures.BMC BIOINFORMATICS,22(1),14.
MLA	Kong, Lupeng,et al."FALCON2: a web server for high-quality prediction of protein tertiary structures".BMC BIOINFORMATICS 22.1(2021):14.