Structural search and retrieval using a tableau representation of protein folding patterns

Arun S. Konagurthu, Peter J. Stuckey, Arthur Lesk

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Comparison and classification of folding patterns from a database of protein structures is crucial to understand the principles of protein architecture, evolution and function. Current search methods for proteins with similar folding patterns are slow and computationally intensive. The sharp growth in the number of known protein structures poses severe challenges for methods of structural comparison. There is a need for methods that can search the database of structures accurately and rapidly. We provide several methods to search for similar folding patterns using a concise tableau representation of proteins that encodes the relative geometry of secondary structural elements. Our first approach allows the extraction of identical and very closely-related protein folding patterns in constant-time (per hit). Next, we address the hard computational problem of extraction of maximally-similar subtableaux, when comparing two tableaux. We solve the problem using Quadratic and Linear integer programming formulations and demonstrate their power to identify subtle structural similarities, especially when protein structures significantly diverge. Finally, we describe a rapid and accurate method for comparing a query structure against a database of protein domains, TableauSearch. TableauSearch is rapid enough to search the entire structural database in seconds on a standard desktop computer. Our analysis of TableauSearch on many queries shows that the method is very accurate in identifying similarities of folding patterns, even between distantly related proteins.

Original languageEnglish (US)
Pages (from-to)645-651
Number of pages7
JournalBioinformatics
Volume24
Issue number5
DOIs
StatePublished - Mar 1 2008

Fingerprint

Protein folding
Protein Folding
Tableau
Folding
Retrieval
Proteins
Protein
Protein Structure
Databases
Query
Structural Similarity
Linear Programming
Tableaux
Integer Linear Programming
Protein Databases
Time Constant
Diverge
Hits
Search Methods
Entire

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Konagurthu, Arun S. ; Stuckey, Peter J. ; Lesk, Arthur. / Structural search and retrieval using a tableau representation of protein folding patterns. In: Bioinformatics. 2008 ; Vol. 24, No. 5. pp. 645-651.
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Structural search and retrieval using a tableau representation of protein folding patterns. / Konagurthu, Arun S.; Stuckey, Peter J.; Lesk, Arthur.

In: Bioinformatics, Vol. 24, No. 5, 01.03.2008, p. 645-651.

Research output: Contribution to journalArticle

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