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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
Shu-Hsien Sheu1, David R Lancia, Karl H Clodfelter
1Department of Biomedical Engineering and Program in Bioinformatics, Boston University, CA, USA.
Nucleic Acids Research
|December 21, 2004
Summary
PRECISE is a database detailing enzyme-ligand interactions, crucial for understanding enzyme function and designing inhibitors. It maps amino acid residue interactions from the Protein Data Bank (PDB) to aid in drug discovery.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Enzyme-ligand interactions are fundamental to enzyme function, substrate specificity, and inhibitor design.
- Understanding these interactions at the amino acid residue level is critical for biochemical research and drug development.
Purpose of the Study:
- To introduce PRECISE (Predicted and Consensus Interaction Sites in Enzymes), a comprehensive database of enzyme-ligand interactions.
- To provide a resource for analyzing and visualizing amino acid residue interactions within enzyme active sites.
Main Methods:
- Information extracted from enzyme-ligand complexes in the Protein Data Bank (PDB).
- Homologous enzyme chains clustered by EC number and sequence similarity.
- Non-bonded and hydrogen bonding interactions identified and summed across homologous chains.
- Representative enzyme sequences color-coded to show interaction sites.
Main Results:
- The PRECISE database provides detailed interaction data for enzyme residues.
- Color-coded sequences visually represent the total interactions at each amino acid position.
- Users can explore detailed interaction lists by clicking on specific residues.
Conclusions:
- The PRECISE database serves as a valuable tool for studying enzyme binding sites.
- It facilitates a deeper understanding of substrate specificity and aids in the rational design of enzyme inhibitors.
- The resource supports advancements in enzyme engineering and therapeutic development.
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