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Updated: Jul 25, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Recognition templates for predicting adenylate-binding sites in proteins
S Zhao1, G M Morris, A J Olson
1Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Journal of Molecular Biology
|December 18, 2001
Summary
This study introduces recognition templates to identify how proteins bind adenylate. These templates reveal key interactions, aiding in the discovery of specific adenylate-binding sites in proteins.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Protein active sites utilize specific interactions to recognize ligands.
- Recognition templates capture these features for identifying binding sites.
Purpose of the Study:
- To develop a method for deriving recognition templates for adenylate groups.
- To understand the molecular basis of adenylate recognition by proteins.
- To demonstrate the utility of these templates in identifying adenylate-binding sites.
Main Methods:
- A grid-based computational method was employed.
- Diverse nucleotide-binding proteins were analyzed.
- Recognition templates were derived for adenylate groups.
Main Results:
- The derived templates highlight shape complementarity and hydrogen bonding in adenylate binding.
- A crucial steric contact was identified that excludes guanylate.
- The method successfully identified specific adenylate-binding sites in dinucleotide-binding proteins.
Conclusions:
- Recognition templates effectively define the specific binding of adenylate.
- This approach aids in the functional annotation of proteins.
- The method is valuable for discovering and characterizing ligand-binding sites.
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