Methodology article

Tableau-based protein substructure search using quadratic programming

Alex Stivala¹ , Anthony Wirth¹ and Peter J Stuckey^1,2

¹Department of Computer Science and Software Engineering, The University of Melbourne, Melbourne, Victoria 3010, Australia

²NICTA Victoria Laboratories at The University of Melbourne, Melbourne, Victoria, Australia

author email corresponding author email

BMC Bioinformatics 2009, 10:153doi:10.1186/1471-2105-10-153

Published:	19 May 2009

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.