Clique-based algorithms for protein threading with profiles and constraints

Protein threading with profiles in which constraints on dist ances between residues are given is known to be NP-hard. Moreover, a simple algorithm known as CLIQUETHREAD based on efficient reduction to maximum edge-weight clique finding problem has been k nown to be a practical algorithm for solving the protein threading problem with profiles and cons traints. This algorithm is not efficient enough to be applicable to large scale threading prediction. Besides, the algorithm was only presented for profile threading with strict constraints. This paper pr esents a more efficient algorithm FTHREAD for profile threading with strict constraints which is more t han times faster than CLIQUETHREAD for larger proteins. Moreover, we also present a novel practical algorithm NTHREAD for profile threading with non-strict constraints. The comparison of FTHREAD with existing state-of-the-art methods shows that although our algorithm uses a simple threading function, our algorithm performs equally well as these existing methods for protein threading. Besides, our computational experiments for sequence-structure alignments for a number of proteins have shown better results for non-strict constraints threading than protein threading with strict c onstraints. We have also analyzed the effects of using a number of distance constraints.

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