1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap

@article{Caprara20041001OP,
  title={1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap},
  author={Alberto Caprara and Robert D. Carr and Sorin Istrail and Giuseppe Lancia and Brian Walenz},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2004},
  volume={11 1},
  pages={27-52}
}
Protein structure comparison is a fundamental problem for structural genomics, with applications to drug design, fold prediction, protein clustering, and evolutionary studies. Despite its importance, there are very few rigorous methods and widely accepted similarity measures known for this problem. In this paper we describe the last few years of developments on the study of an emerging measure, the contact map overlap (CMO), for protein structure comparison. A contact map is a list of pairs of… CONTINUE READING
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