Recognition templates for predicting adenylate-binding sites in proteins

Shanrong Zhao, Garrett M. Morris, Arthur J. Olson, David S. Goodsell

Research output: Contribution to journalArticle

15 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1245-1255
Number of pages11
JournalJournal of molecular biology
Volume314
Issue number5
DOIs
StatePublished - Dec 14 2001

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All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • Molecular recognition
  • Nucleotide recognition
  • Nucleotide-binding proteins
  • Protein function prediction
  • Protein-ligand docking

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