Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso

Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu

To uncover molecular functions and networks in biological cellular systems, it is important to dissect interactions between proteins and RNAs. Many studies have been performed to investigate and analyze interactions between protein amino acid residues and RNA bases. In terms of interactions between residues in proteins, it is generally accepted that an amino acid residue at interacting sites has coevolved together with the partner residue in order to keep the interaction between residues in proteins. Based on this hypothesis, in our previous study to identify residue-residue contact pairs in interacting proteins, we made calculations of mutual information (M I) between amino acid residues from some multiple sequence alignment of homologous proteins, and combined it with a discriminative random field (DRF) approach, which is a special type of conditional random fields (CRFs) and has been proved useful for the purpose of extracting distinguishing areas from a photograph in the image processing field. Recently, the evolutionary correlation of interactions between residues and DNA bases has also been found in certain transcription factors and the DNA-binding sites.