In Silico Footprinting of Ligands Binding to the Minor Groove of DNA
Anthony, N.G. and Huchet, G. and Johnston, B.F. and Parkinson, B.F. and Suckling, C.J. and Waigh, R.D. and Mackay, S.P. (2005) In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. Journal of Chemical Information and Modeling, 45 (6). pp. 1896-1907. ISSN 1549-9596 (http://dx.doi.org/10.1021/ci050153b)
Full text not available in this repository.Request a copyAbstract
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.
ORCID iDs
Anthony, N.G.


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Item type: Article ID code: 816 Dates: DateEvent5 October 2005PublishedKeywords: Silico Footprinting, Ligands Binding, Minor Groove, DNA, energy minimization, noncovalent binding modes, X-ray crystallography, Chemistry, Chemical Engineering(all), Chemistry(all), Library and Information Sciences, Computer Science Applications Subjects: Science > Chemistry Department: Faculty of Science > Pure and Applied Chemistry
Faculty of Science > Strathclyde Institute of Pharmacy and Biomedical Sciences
Unknown DepartmentDepositing user: Users 41 not found. Date deposited: 20 Apr 2006 Last modified: 19 May 2023 01:05 URI: https://strathprints.strath.ac.uk/id/eprint/816