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Protein fold comparison by the alignment of topological strings
Linus O Johannissen1, William R Taylor
1Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
Protein Engineering
|February 26, 2004
Summary
A novel dynamic programming algorithm compares protein folds by identifying common substructures and calculating distances. This method creates a protein
Area of Science:
- Computational biology
- Structural bioinformatics
- Protein science
Background:
- Protein structure comparison is crucial for understanding protein function and evolution.
- Existing methods for clustering protein folds have limitations in representing ancestral states.
Purpose of the Study:
- To develop a novel algorithm for comparing protein folds and constructing a phylogenetic tree.
- To identify the largest common substructure between protein folds and quantify structural distances.
Main Methods:
- A dynamic programming algorithm was used to compare protein folds represented as text strings.
- The algorithm identifies the largest common substructure and calculates edit distances between folds.
- Protein folds were clustered into a phylogenetic tree based on these calculated distances.
Main Results:
- The algorithm successfully clustered protein folds into a phylogenetic tree with explicit representation of ancestral nodes.
- Comparison with an expert-compiled tree showed broad agreement but highlighted differences in the emphasis of structural transformation operations.
- The generated tree offers a new perspective on protein fold relationships.
Conclusions:
- The developed algorithm provides a novel approach to protein fold comparison and phylogenetic tree construction.
- The method's ability to represent ancestral structures offers insights into protein evolution.
- Further research can explore the implications of this tree for protein folding mechanisms and evolutionary history.