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Protein structural topology: Automated analysis and diagrammatic representation.
D R Westhead1, T W Slidel, T P Flores
1The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. westhead@bmb.leeds.ac.uk
Protein Science : a Publication of the Protein Society
|April 22, 1999
Summary
A new algorithm generates protein topology diagrams (TOPS cartoons) more reliably than before. This tool aids in understanding and comparing protein structures, creating a comprehensive database of these essential diagrams.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Protein topology simplifies complex protein structures by detailing secondary structure elements and their spatial relationships.
- TOPS (Topology of Protein Structure) cartoons are 2D diagrams effectively representing protein topology, aiding in fold comprehension and comparison.
- Existing algorithms for generating TOPS cartoons have limitations in robustness and success rates.
Purpose of the Study:
- To introduce a novel, more robust algorithm for generating protein topology diagrams (TOPS cartoons).
- To enhance the accuracy and success rate of creating these simplified protein structure representations.
- To build a comprehensive database of TOPS cartoons for known protein structures.
Main Methods:
- Development of a new computational algorithm for analyzing protein structures.
- Implementation of the algorithm to process and generate 2D TOPS cartoons.
- Application of the algorithm to a large dataset of protein structures from the Protein Data Bank.
Main Results:
- The new algorithm demonstrates significantly improved robustness and a higher success rate in generating TOPS cartoons.
- A comprehensive database of protein topology cartoons has been successfully produced, covering a majority of known protein structures.
- The generated cartoons facilitate easier understanding and comparison of diverse protein folds.
Conclusions:
- The developed algorithm offers a superior method for creating protein topology diagrams.
- The resulting database serves as a valuable resource for researchers studying protein structure and evolution.
- This advancement improves the accessibility and utility of topological information in structural biology.