DMCA
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints ∗ (2006)
BibTeX
@MISC{†a06dynamicprogramming,
author = {Tatsuya Akutsu †a and Morihiro Hayashida and Dukka Bahadur K. C and Etsuji Tomita and Katsuhisa Horimoto},
title = {Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints ∗},
year = {2006}
}
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Abstract
SUMMARY The protein threading problem with profiles is known to be efficiently solvable using dynamic programming. In this paper, we consider a variant of the protein threading problem with profiles in which constraints on distances between residues are given. We prove that protein threading with profiles and constraints is NP-hard. Moreover, we show a strong hardness result on the approximation of an optimal threading satisfying all the constraints. On the other hand, we develop two practical algorithms: CLIQUETHREAD and BBDPTHREAD. CLIQUETHREAD reduces the threading problem to the maximum edgeweight clique problem, whereas BBDPTHREAD combines dynamic programming and branch-and-bound techniques. We perform computational experiments using protein structure data in PDB (Protein Data Bank) using simulated distance constraints. The results show that constraints are useful to improve the alignment accuracy of the target sequence and the template structure. Moreover, these results also show that BBDPTHREAD is in general faster than CLIQUETHREAD for larger size proteins whereas CLIQUETHREAD is useful if there does not exist a feasible threading. key words: maximum edge weight clique, dynamic programming, protein threading, profiles, distance constraints 1.
Keyphrases
dynamic programming distance constraint size protein whereas cliquethread computational experiment bbdpthread combine dynamic programming target sequence branch-and-bound technique protein data bank template structure protein structure data practical algorithm maximum edgeweight clique problem threading problem general faster optimal threading feasible threading protein threading strong hardness result key word alignment accuracy maximum edge weight clique
