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Computational Design of Ligand Binding Proteins

Volume 1414 of the series Methods in Molecular Biology pp 353-372

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Modeling of Protein–RNA Complex Structures Using Computational Docking Methods

  • Bharat MadanAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
  • , Joanna M. KasprzakAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in WarsawBioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University
  • , Irina TuszynskaAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in WarsawInstitute of Informatics, University of Warsaw
  • , Marcin MagnusAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
  • , Krzysztof SzczepaniakAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
  • , Wayne K. DawsonAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
  • , Janusz M. BujnickiAffiliated withLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in WarsawBioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Email author 

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Abstract

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.

Key words

Protein–RNA docking NPDock Molecular modeling Macromolecular complexes Structural bioinformatics Statistical potential