Prediction of dinucleotide-specific RNA-binding sites in proteins.

ABSTRACT:

Background

Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach.

Results

We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferenc

SUBMITTER: Fernandez M 

PROVIDER: S-EPMC3278845 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature