Methods and applications of RNA contact prediction

doi:10.1088/1674-1056/abb7f3

摘要/Abstract

Abstract:

The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational modeling. One promising approach is first to predict the tertiary contacts and then use the contacts as constraints to model the structure. The RNA structure modeling depends on the contact prediction accuracy. Although many contact prediction methods have been developed in the protein field, there are only several contact prediction methods in the RNA field at present. Here, we first review the theoretical basis and test the performances of recent RNA contact prediction methods for tertiary structure and complex modeling problems. Then, we summarize the advantages and limitations of these RNA contact prediction methods. We suggest some future directions for this rapidly expanding field in the last.

Key words: RNA structure, contact prediction, direct coupling analysis, network, machine learning

中图分类号: (RNA)

87.14.gn

87.15.K- (Molecular interactions; membrane-protein interactions) 87.10.Ca (Analytical theories) 87.15.A- (Theory, modeling, and computer simulation)

Huiwen Wang(王慧雯), Yunjie Zhao(赵蕴杰). [J]. 中国物理B, 2020, 29(10): 108708-.

Huiwen Wang(王慧雯) and Yunjie Zhao(赵蕴杰)†. Methods and applications of RNA contact prediction[J]. Chin. Phys. B, 2020, 29(10): 108708-.

图/表 6

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Method name	Input information	Comments	Link	Reference
Mutual Information	RNA sequence	intramolecular contacts	http://dca.rice.edu/portal/dca/home	[64–66]
mpDCA	RNA sequence	intramolecular contacts	not available	[77]
mfDCA	RNA sequence	intramolecular contacts	http://dca.rice.edu/portal/dca/home	[74]
plmDCA	RNA sequence	intramolecular contacts	https://github.com/magnusekeberg/plmDCA	[78]
DIRECT	RNA sequence and structure	intramolecular contacts	https://zhaolab.com.cn/DIRECT/	[79]
Rsite	RNA structure	intermolecular contacts	http://www.cuilab.cn/rsite	[85]
Rsite2	RNA structure	intermolecular contacts	http://www.cuilab.cn/rsite2	[86]
RBind	RNA structure	intermolecular contacts	https://zhaolab.com.cn/RBind/	[87]
PRIdictor	RNA and protein sequences	intermolecular contacts	http://bclab.inha.ac.kr/pridictor/	[89]