From sequence to structure and back again: approaches for predicting protein-DNA binding

Gene regulation in higher organisms is achieved by a complex network of transcription factors (TFs). Modulating gene expression and exploring gene function are major aims in molecular biology. Furthermore, the identification of putative target genes for a certain TF serve as powerful tools for specific targeting of rational drugs. Detecting the short and variable transcription factor binding sites (TFBSs) in genomic DNA is an intriguing challenge for computational and structural biologists. Fast and reliable computational methods for predicting TFBSs on a whole-genome scale offer several advantages compared to the current experimental methods that are rather laborious and slow. Two main approaches are being explored, advanced sequence-based algorithms and structure-based methods. The aim of this review is to outline the computational and experimental methods currently being applied in the field of protein-DNA interactions. With a focus on the former, the current state of the art in modeling these interactions is discussed. Surveying sequence and structure-based methods for predicting TFBSs, we conclude that in order to achieve a sound and specific method applicable on genomic sequences it is desirable and important to bring these two approaches together.