Efficient labelling algorithms for the maximum noncrossing matching problem
Discrete Applied Mathematics - Special issue on new frontiers in the theory and practice of combinatorial optimization: applications in manufacturing and VLSI design
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Structural alignment of large—size proteins via lagrangian relaxation
Proceedings of the sixth annual international conference on Computational biology
Alignment Of Protein Structures With A Memetic Evolutionary Algorithm
GECCO '02 Proceedings of the Genetic and Evolutionary Computation Conference
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case
Genetic Programming and Evolvable Machines
Optimal Protein Structure Alignment Using Maximum Cliques
Operations Research
Pairwise global alignment of protein interaction networks by matching neighborhood topology
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Multiple alignment of contact maps
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
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Bimal, a fast method for approximately solving the maximum contact map overlap (maxCMO) problem is introduced. The method is based on an approximate model of the maxCMO-problem using the generic bipartite graph matching framework, which is then optimally solved by double dynamic programming. The performance of Bimal has been evaluated in an empirical comparative study including clustering of protein structures according to the SCOP fold's level. Solving about 800 pairwise alignments of medium-sized proteins takes less than 1 min on a 1.7 GHz machine and yields good results for similar protein structures. Bimal accurately classified proteins in agreement with the SCOP classification. In particular, for similar proteins, Bimal provides a good tradeoff between computation speed and solution quality and is because of its high speed useful for solving large-scaled maxCMO applications.