ArticleBMC bioinformatics2009
Tableau-based protein substructure search using quadratic programming.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.BMC bioinformatics · 2016Article
- Multiple graph regularized protein domain ranking.BMC bioinformatics · 2012Article
- BetaSearch: a new method for querying β-residue motifs.BMC research notes · 2012Article
- ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.BMC bioinformatics · 2012Article
- Rigid substructure search.Bioinformatics (Oxford, England) · 2011Article
- Fast and accurate protein substructure searching with simulated annealing and GPUs.BMC bioinformatics · 2010Article
- A fast indexing approach for protein structure comparison.BMC bioinformatics · 2010Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSearching 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.
resultsWe 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.
conclusionWe 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.
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