Integer and combinatorial optimization
Integer and combinatorial optimization
A lift-and-project cutting plane algorithm for mixed 0-1 programs
Mathematical Programming: Series A and B
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Exact Solution of the Quadratic Knapsack Problem
INFORMS Journal on Computing
A Heuristic Method for the Set Covering Problem
Operations Research
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Integer programming models for computational biology problems
Journal of Computer Science and Technology - Special issue on bioinformatics
A Demonstration of Clustering in Protein Contact Maps for Alpha Helix Pairs
ICANNGA '07 Proceedings of the 8th international conference on Adaptive and Natural Computing Algorithms, Part I
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Evaluating Protein Similarity from Coarse Structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On Protein Structure Alignment under Distance Constraint
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
Bimal: bipartite matching alignment for the contact map overlap problem
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
A fuzzy sets based generalization of contact maps for the overlap of protein structures
Fuzzy Sets and Systems
The Journal of Machine Learning Research
Joining softassign and dynamic programming for the contact map overlap problem
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
A propagator for maximum weight string alignment with arbitrary pairwise dependencies
CP'10 Proceedings of the 16th international conference on Principles and practice of constraint programming
A similarity matrix-based hybrid algorithm for the contact map overlaps problem
Computers in Biology and Medicine
On protein structure alignment under distance constraint
Theoretical Computer Science
Fast and accurate structural RNA alignment by progressive lagrangian optimization
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
Multiple structural RNA alignment with lagrangian relaxation
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Structural alignment of two RNA sequences with lagrangian relaxation
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A branch-and-reduce algorithm for the contact map overlap problem
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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We illustrate a new approach to the Contact Map Overlap problem for the comparison of protein structures. The approach is based on formulating the problem as an integer linear program and then relaxing in a Lagrangian way a suitable set of constraints. This relaxation is solved by computing a sequence of simple alignment problems, each in quadratic time, and near--optimal Lagrangian multipliers are found by subgradient optimization. By our approach we achieved a substantial speedup over the best existing methods. We were able to solve optimally for the first time instances for PDB proteins with about 1000 residues and 2000 contacts. Moreover, within a few hours we compared 780 pairs in a testbed of 40 large proteins, finding the optimal solution in 150 cases. Finally, we compared 10,000 pairs of proteins from a test set of 269 proteins in the literature, which took a couple of days on a PC.