%0 Online Multimedia %A Anthony, Nahoum G. %A Huchet, Guillaume %A Johnston, Blair F. %A Parkinson, John A. %A Suckling, Colin J. %A Waigh, Roger D. %A Mackay, Simon P. %D 2005 %T In Silico Footprinting of Ligands Binding to the Minor Groove of DNA %U https://acs.figshare.com/articles/media/In_Silico_Footprinting_of_Ligands_Binding_to_the_Minor_Groove_of_DNA/3254554 %R 10.1021/ci050153b.s003 %2 https://acs.figshare.com/ndownloader/files/5089924 %K molecules binding %K Ligands Binding %K sequence selectivity %K Silico Footprinting %K Minor Groove %K energy minimization %K footprinting %K show application %K noncovalent binding modes %K NMR %K hairpin ligands %K binding site %K simulation techniques %K DNA base pair sequences %K groove %X The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by “in silico footprinting”. Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting. %I ACS Publications