Using 3dRPC for RNA–protein complex structure prediction

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.