title: PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties.
abstract: The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php.
authors.affiliation: Department for Molecular Biomedical Research, VIB, Ghent University, B-9052 Ghent, Belgium.
authors.forename: Stefan
authors.initials: S
authors.lastname: Broos
authors.forename: Arne
authors.initials: A
authors.lastname: Soete
authors.forename: Bart
authors.initials: B
authors.lastname: Hooghe
authors.forename: Raymond
authors.initials: R
authors.lastname: Moran
authors.forename: Frans
authors.initials: F
authors.lastname: van Roy
authors.forename: Pieter
authors.initials: P
authors.lastname: De Bleser
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D020407:Internet; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D012984:Software; D019098:Telomerase / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA; C509186:TERT protein, human; D019098:Telomerase