Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

Genes
Chandran NithinJanusz M Bujnicki

Abstract

RNA-protein (RNP) interactions play essential roles in many biological processes, such as regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing, transport, storage and stabilization, as well as protein synthesis. An increasing number of RNP structures would aid in a better understanding of these processes. However, due to the technical difficulties associated with experimental determination of macromolecular structures by high-resolution methods, studies on RNP recognition and complex formation present significant challenges. As an alternative, computational prediction of RNP interactions can be carried out. Structural models obtained by theoretical predictive methods are, in general, less reliable compared to models based on experimental measurements but they can be sufficiently accurate to be used as a basis for to formulating functional hypotheses. In this article, we present an overview of computational methods for 3D structure prediction of RNP complexes. We discuss currently available methods for macromolecular docking and for scoring 3D structural models of RNP complexes in particular. Additionally, we also review benchmarks that have been developed to assess the accuracy of these methods.

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Citations

Aug 10, 2019·RNA·Chandran NithinRanjit Prasad Bahadur
Sep 24, 2020·International Journal of Molecular Sciences·Kui WangLukasz Kurgan
Apr 10, 2020·Nature Protocols·Yumeng YanSheng-You Huang
Jun 10, 2020·Computational and Structural Biotechnology Journal·Jorge Roel-Touris, Alexandre M J J Bonvin
Apr 19, 2019·Current Opinion in Structural Biology·Ilya A Vakser, Eric J Deeds
Mar 26, 2021·Journal of Chemical Theory and Computation·Roy González-AlemánFabrice Leclerc
Aug 25, 2020·Current Opinion in Structural Biology·Ilya A Vakser
Dec 10, 2020·Journal of Chemical Information and Modeling·Yuyu Feng, Sheng-You Huang
Sep 2, 2021·Journal of Chemical Information and Modeling·Yuyu FengSheng-You Huang
Dec 21, 2021·Briefings in Bioinformatics·Junkang WeiYu Li

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Methods Mentioned

BETA
X-ray
electron microscopy
nuclear
electron paramagnetic resonance
NMR

Software Mentioned

HHSuite
DECK
DARS
Integrative Modelling Platform ( IMP )
mCSM
PyRy3D
RPRANK
FILTREST3D
pyDock
PRince webserver

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