A Computational Approach for the Discovery of Protein-RNA Networks

Methods Mol Biol. 2016;1358:29-39. doi: 10.1007/978-1-4939-3067-8_2.


Protein-RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present the computational approach catRAPID to predict protein-RNA interactions and discuss how it could be used to find trends in ribonucleoprotein networks. We envisage that the combination of computational and experimental approaches will be crucial to unravel the role of coding and noncoding RNAs in protein networks.

Keywords: Interaction prediction; Messenger RNA; Noncoding RNA; Protein–RNA interactions; Ribonucleoprotein networks; catRAPID.

MeSH terms

  • Computational Biology / methods*
  • Gene Expression Regulation / genetics*
  • Gene Regulatory Networks
  • RNA, Long Noncoding / genetics
  • RNA, Messenger / genetics
  • RNA-Binding Proteins / genetics*
  • Ribonucleoproteins / genetics*
  • Software


  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribonucleoproteins