Tableau-based protein substructure search using quadratic programming.
Alex Stivala, Anthony Wirth, Peter J Stuckey
BMC Bioinformatics | Published : 2009
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 fin..View full abstract