Abstract
In this paper we present a graph-theoretical method for computing the maximum orthogonal subset of a set of coiled-coil peptides. In chemistry, an orthogonal set of peptides is defined as a set of pairs of peptides, where the paired peptides interact only mutually and not with any other peptide from any other pair. The main method used is a reduction to the maximum independent set problem. Then we use a relatively well-known maximum independent set solving algorithm which turned out to be the best suited for our problem. We obtained an orthogonal set consisting of 29 peptides (homodimeric and heterodimeric) from initial 5-heptade set. If we allow only heterodimeric interactions we obtain an orthogonal set of 26 peptides.
Highlights
Povzetek: V clanku je predstavljen izracun najvecje ortogonalne množice peptidov z uporabo metod teorije grafov
We describe a method for determining an orthogonal set of maximum size, from a given set of admissible peptides
Combining the NP-hardness with the earlier fact that MISP is in NP, we conclude that MISP is NPcomplete
Summary
As input we are given a set of peptides P = p1, p2, . Pn (their primary structures – given as strings of fixed length) and interaction matrix I. If i = j in (pi, pj) we are talking of homodimer and otherwise of heterodimer. We can model this problem as a graph-theoretical one: First, an undirected graph G = (V, E) where V is the set of peptides P , and the edge set E contains an edge pipj (or a loop at pi, denoted by pipi) if and only if pi and pj interact. We want to find a subset of non-adjacent edges whose vertices are non-adjacent. Does there exist set a S ⊆ E such that for any u1v1, u2v2 ∈ S
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