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  • Title: Recognition templates for predicting adenylate-binding sites in proteins.
    Author: Zhao S, Morris GM, Olson AJ, Goodsell DS.
    Journal: J Mol Biol; 2001 Dec 14; 314(5):1245-55. PubMed ID: 11743737.
    Abstract:
    Recognition templates encapsulate the structural and energetic features for the specific recognition of a given ligand by a protein active site. These templates identify the major interactions used for specific recognition and may be used to find specific binding sites in proteins of unknown function. We present a grid-based method for deriving recognition templates for adenylate groups from a set of diverse nucleotide-binding proteins. The templates reveal the basis of specific binding of adenylate, including tight shape complementarity, specific hydrogen bonds, and underscoring the importance of a key steric contact for excluding guanylate from adenylate-specific sites. We demonstrate the utility of recognition templates in identifying specific adenylate-binding sites in a diverse set of dinucleotide-binding proteins.
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