Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.
A significant part of biology involves the formation of RNA-protein complexes. X-ray crystallography has added a few solved RNA-protein complexes to the repertoire; however, it remains challenging to capture these complexes and often only the unbound structures are available. This has inspired a growing interest in finding ways to predict these RNA-protein complexes. In this study, we show ways to approach this problem by computational docking methods, either with a fully automated NPDock server or with a workflow of methods for generation of many alternative structures followed by selection of the most likely solution. We show that by introducing experimental information, the structure of the bound complex is rendered far more likely to be within reach. This study is meant to help the user of docking software understand how to grapple with a typical realistic problem in RNA-protein docking, understand what to expect in the way of difficulties, and recognize the current limitations.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
Bharat
B
Madan
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.|Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
Joanna M
JM
Kasprzak
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.|Institute of Informatics, University of Warsaw, ul. Banacha 2, 02-097, Warsaw, Poland.
Irina
I
Tuszynska
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
Marcin
M
Magnus
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
Krzysztof
K
Szczepaniak
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
Wayne K
WK
Dawson
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland. iamb@genesilico.pl.|Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland. iamb@genesilico.pl.
Janusz M
JM
Bujnicki
D062105:Molecular Docking Simulation; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012984:Software
D011506:Proteins; D012313:RNA
Macromolecular complexes; Molecular modeling; NPDock; Protein–RNA docking; Statistical potential; Structural bioinformatics