If you are interested in the works at the base of Nucleos here you can find the proper bibliography (please cite us if you make use of Nucleos)
Identification of nucleotide-binding sites in protein structures
Luca Parca, Pier Federico Gherardini, Mauro Truglio, Iolanda Mangone, Fabrizio Ferré, Manuela Helmer-Citterich and Gabriele Ausiello (2012) Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. Plos ONE (in press).Modularity of nucleotide and their binding sites
Pier Federico Gherardini, Gabriele Ausiello, Robert B. Russell and Manuela Helmer-Citterich (2010) Modular architecture of nucleotide-binding pockets. Nucleic Acids Res 38 (11): 3809-3816.Identification of phosphate-binding sites in protein structures
Luca Parca, Pier Federico Gherardini, Manuela Helmer-Citterich and Gabriele Ausiello (2011) Phosphate binding sites identification in protein structures. Nucleic Acids Res., 39 (4): 1231-1242.