ThreaDNA
ThreaDNA is a bioinformatics tool that efficiently predicts genomic binding sites for the user's protein of interest, based on DNA mechanical distortions.
Link to the original publication in BioinformaticsIt takes high-resolution structures of the protein-DNA complex as input, and provides the deformation energy profile along entire genomes at basepair resolution within minutes on an usual computer. This deformation energy plays a major role in indirect sequence recognition by many proteins, such as eurakyotic histones, bacterial nucleoid-associated proteins and transcriptional regulators, e.g. Fis and CRP.
The current stable version of the software is available here.
The code is under development in the GitHub repository ThreaDNA.
A webserver version is accessible via the Galaxy platform of bioinfo@insa-lyon.
