Prediction of interacting single-stranded RNA bases by protein-binding patterns.

ABSTRACT: Prediction of protein-RNA interactions at the atomic level of detail is crucial for our ability to understand and interfere with processes such as gene expression and regulation. Here, we investigate protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. We observed that most of the protein-interacting nucleotides are part of a consecutive fragment of at least two nucleotides whose rings have significant interactions with the protein. Many of these share the same protein binding cavity and more than 30% of such pairs are pi-stacked. Since these local geometries cannot be inferred from the nucleotide identities, we present a novel framework for their prediction from the properties of protein binding sites. First, we present a classification of known

SUBMITTER: Shulman-Peleg A 

PROVIDER: S-EPMC2429989 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature