Tableau-based protein substructure search using quadratic programming

Alex Stivala, Anthony Wirth, Peter J. Stuckey

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

Abstract

Background: Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database. Results: We developed an improved method for detecting substructural similarities in proteins using tableaux. Tableaux are compared efficiently by solving the quadratic program (QP) corresponding to the quadratic integer program (QIP) formulation of the extraction of maximally-similar tableaux. We compare the accuracy of the method in classifying protein folds with some existing techniques. Conclusion: We find that including constraints based on the separation of secondary structure elements increases the accuracy of protein structure search using maximally-similar subtableau extraction, to a level where it has comparable or superior accuracy to existing techniques. We demonstrate that our implementation is able to search a structural database in a matter of hours on a standard PC.

Original languageEnglish
Article number153
Number of pages21
JournalBMC Bioinformatics
Volume10
DOIs
Publication statusPublished - 19 May 2009
Externally publishedYes

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