Prediction of RNA binding residues: An extensive analysis based on structure and function to select the best predictor

Abstract

Protein-RNA complexes play key roles in several cellular processes by the interactions of amino acids with RNA. To understand the recognition mechanism, it is important to identify the specific amino acids involved in RNA binding. Various computational methods have been developed for predicting RNA binding residues from protein sequence. However, their performances mainly depend on the training dataset, feature selection for developing a model and learning capacity of the model. Hence, it is important to reveal the correspondence between the performance of methods and properties of RNA-binding proteins (RBPs). In this work, we have collected all available RNA binding residues prediction methods and revealed their performances on unbiased, stringent and diverse datasets for RBPs with less than 25% sequence identity based on structural class, fold, superfamily, family, protein function, RNA type, RNA strand and RNA conformation. The best methods for each type of RBPs and the type of RBPs, which require further refinement in prediction, have been brought out. We also analyzed the performance of these methods for the disordered regions, structures which are not included in the training dataset and recently solved structures. The reliability of prediction is better than randomly choosing any method or combination of methods. This approach would be a valuable resource for biologists to choose the best method based on the type of RBPs for designing their experiments and the tool is freely accessible online at www.iitm.ac.in/bioinfo/RNAprotein/. © 2014 Nagarajan, Gromiha.