Predicting nucleic acid binding interfaces from structural models of proteins.

ABSTRACT: The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches ext

SUBMITTER: Dror I 

PROVIDER: S-EPMC3290761 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature