Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.

ABSTRACT: An RNA-binding protein places a surface helix, beta-ribbon, or loop in an RNA helix groove and/or uses a cavity to accommodate unstacked bases. Hence, our strategy for predicting RNA-binding residues is based on detecting a surface patch and a disparate cleft. These were generated and scored according to the gas-phase electrostatic energy change upon mutating each residue to Asp(-)/Glu(-) and each residue's relative conservation. The method requires as input the protein structure and sufficient homologous sequences to define each residue's relative conservation. It yields as output a priority list of surface patch residues followed by a backup list of surface cleft residues distant from the patch residues for experimental testing of RNA binding. Among the 69 structurally non-homologous pro

SUBMITTER: Chen YC 

PROVIDER: S-EPMC2275128 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature