Using 3dRPC for RNA-protein complex structure prediction

Yangyu Huang; Haotian Li; Yi Xiao

doi:10.1007/s41048-017-0034-y

Using 3dRPC for RNA-protein complex structure prediction

Biophys Rep. 2016;2(5):95-99. doi: 10.1007/s41048-017-0034-y. Epub 2017 Feb 10.

Authors

Yangyu Huang¹, Haotian Li¹, Yi Xiao¹

Affiliation

¹ Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074 China.

Abstract

3dRPC is a computational method designed for three-dimensional RNA-protein complex structure prediction. Starting from a protein structure and a RNA structure, 3dRPC first generates presumptive complex structures by RPDOCK and then evaluates the structures by RPRANK. RPDOCK is an FFT-based docking algorithm that takes features of RNA-protein interactions into consideration, and RPRANK is a knowledge-based potential using root mean square deviation as a measure. Here we give a detailed description of the usage of 3dRPC. The source code is available at http://biophy.hust.edu.cn/3dRPC.html.

Keywords: Computational prediction; Docking; RNA–protein complex; Scoring function; Tertiary structure.