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A computer system to perform structure comparison using TOPS representations of protein structure.

D Gilbert1, D Westhead, J Viksna

  • 1Department of Computing, City, University, Northampton Square, London EC1V 0HB, UK. drg@soi.city.ac.uk

Computers & Chemistry
|January 5, 2002
PubMed
Summary

This study introduces a rapid, topology-based protein structure comparison method using the TOPS representation. It enables efficient alignment and distance measurement for large-scale protein structure analysis.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure comparison is crucial for understanding function and evolution.
  • Existing methods can be computationally intensive for large datasets.

Purpose of the Study:

  • To develop and implement a fast, topology-based method for protein structure comparison.
  • To provide a web-accessible tool for comparing protein structures against the Protein Data Bank.

Main Methods:

  • Utilizes the TOPS (TOpological Protein Structure) representation for protein structure.
  • Employs a constraint-based pattern-matching algorithm for aligning TOPS diagrams.
  • Calculates a distance measure based on an insert score.

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Main Results:

  • A fast and efficient topology-based protein structure comparison system has been designed and implemented.
  • The system successfully aligns protein structures using discovered common patterns.
  • A web server is available for public use, allowing comparison against the entire PDB.

Conclusions:

  • The developed method offers a computationally efficient approach to protein structure comparison.
  • The web-accessible tool facilitates large-scale analysis of protein structural relationships.
  • This method aids in understanding protein function and evolutionary connections through structural similarity.