Alberto Caprara
ABSTRACT
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.
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Index Terms
- Structural alignment of large—size proteins via lagrangian relaxation
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