Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

ABSTRACT: Predicting the binding specificity of transcription factors is a critical step in the characterization and computational identification and of cis-regulatory elements in genomic sequences. Here we use protein-DNA structures to predict binding specificity and consider the possibility of predicting position weight matrices (PWM) for an entire protein family based on the structures of just a few family members. A particular focus is the sensitivity of prediction accuracy to the docking geometry of the structure used. We investigate this issue with the goal of determining how similar two docking geometries must be for binding specificity predictions to be accurate. Docking similarity is quantified using our recently described interface alignment score (IAS). Using a molecular-mechanics force f

SUBMITTER: Siggers TW 

PROVIDER: S-EPMC1851644 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature