Protein-RNA Docking Using ICM

Journal of Chemical Theory and Computation
Yelena A ArnautovaMaxim Totrov

Abstract

Protein-RNA interactions play an important role in many biological processes. Computational methods such as docking have been developed to complement existing biophysical and structural biology techniques. Computational prediction of protein-RNA complex structures includes two steps: generating candidate structures from the individual protein and RNA parts and scoring the generated poses to pick out the correct one. In this work, we considered three recently developed data sets of protein-RNA complexes to evaluate and improve the performance of the FFT-based rigid-body docking algorithm implemented in the ICM package. An electrostatic term describing interactions between negatively charged phosphate groups and positively charged protein residues was added to the energy function used during the docking step to take into account the greater role that electrostatic interactions play in protein-RNA complexes. Next, the docking results were used to optimize a scoring function including van der Waals, electrostatic, and solvation terms. This optimization yielded a much smaller weight for the solvation term indicating that solvation energy may be less important for the scoring of protein-RNA structures. Rescoring of the generated pose...Continue Reading

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Citations

Oct 11, 2019·Nucleic Acids Research·Nina KolchinaMichael Petukhov
Nov 17, 2019·Proceedings of the National Academy of Sciences of the United States of America·Javier Delgado BlancoLuis Serrano
Apr 19, 2019·Current Opinion in Structural Biology·Ilya A Vakser, Eric J Deeds

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