Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.

@article{Siggers2005StructuralAO,
  title={Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.},
  author={Trevor W. Siggers and Antonina Silkov and Barry Honig},
  journal={Journal of molecular biology},
  year={2005},
  volume={345 5},
  pages={1027-45}
}
A new method is introduced to structurally align interfaces observed in protein--DNA complexes. The method is based on a procedure that describes the interfacial geometry in terms of the spatial relationships between individual amino acid--nucleotide pairs. An amino acid--amino acid similarity matrix, S, is defined that provides a quantitative measure of the geometric relationships of amino acids in different interfaces and the entire stretch of "local" DNA within some distance of each amino… CONTINUE READING