Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
Computing Largest Common Point Sets under Approximate Congruence
ESA '00 Proceedings of the 8th Annual European Symposium on Algorithms
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Finding Largest Well-Predicted Subset of Protein Structure Models
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Algorithms for optimal protein structure alignment
Bioinformatics
On Complexity of Protein Structure Alignment Problem under Distance Constraint
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
DALIX: Optimal DALI Protein Structure Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Improved Algorithms for Matching r-Separated Sets with Applications to Protein Structure Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Protein structure alignment is an important tool in many biological applications, such as protein evolution studies, protein structure modeling, and structure-based, computer-aided drug design. Protein structure alignment is also one of the most challenging problems in computational molecular biology, due to an infinite number of possible spatial orientations of any two protein structures. We study one of the most commonly used measures of pairwise protein structure similarity, defined as the number of pairs of atoms in two proteins that can be superimposed under a predefined distance cutoff. We prove that the expected running time of a recently published algorithm for optimizing this (and some other, derived measures of protein structure similarity) is polynomial.