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.
Highlights
RNA–protein interactions have drawn much attention recently since they might play important roles in many biological processes (Chen and Varani 2005; Glisovic et al 2008)
As the protein–protein interactions, the three-dimensional structures of RNA–protein complexes are essential to understand the mechanism of RNA–protein interactions
RPRANK extracts the residue-base pairs within 10 Å, and the pairs from decoy complexes are compared with standard pairs that are from native structures
Summary
RNA–protein interactions have drawn much attention recently since they might play important roles in many biological processes (Chen and Varani 2005; Glisovic et al 2008). It was found that most of the human genome could be transcribed into RNAs but only a small fraction of these RNAs was translated into proteins (Cheng et al 2005), i.e., most RNAs did not undergo translation These non-coding RNAs perform their biological functions mostly through RNA–protein interactions and forming RNA–protein complexes. Most algorithms for predicting complex structure consist of two stages: sampling and scoring. The scoring function DECK-RP has been replaced in the updated 3dRPC by RPRANK, a new knowledge-based potential using Root mean square deviation (RMSD) as a measure. The statistical objects of RPRANK are the conformation differences between residue-base pairs. RPRANK extracts the residue-base pairs within 10 Å, and the pairs from decoy complexes are compared with standard pairs that are from native structures.
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