Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.

@article{Kupas2008LargeSA,
  title={Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.},
  author={Katrin Kupas and Alfred Ultsch and Gerhard Klebe},
  journal={Proteins},
  year={2008},
  volume={71 3},
  pages={1288-306}
}
A new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent-accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape… CONTINUE READING

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