Construction of orthogonal CC-sets

Authors

  • Andrej Brodnik University of Primorska
  • Vladan Jovičić École Normale Supérieure
  • Marko Palangetić University of Primorska
  • Daniel Silađi University of Primorska

DOI:

https://doi.org/10.31449/inf.v43i1.2693

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.

References

M. Depolli, J. Konc, K. Rozman, R. Trobec, and D. Janezic. Exact parallel maximum clique algorithm for general and protein graphs. Journal of chemical information and modeling, 53(9):2217–2228, 2013.

H. Gradišar, S. Božič, T. Doles, D. Vengust, I. Hafner-Bratkovič, A. Mertelj, B. Webb, A. Šali, S. Klavžar, and R. Jerala. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nature chemical biology, 9(6):362–366, 2013.

V. Potapov, J. B. Kaplan, and A. E. Keating. Data-driven prediction and design of bzip coiled-coil interactions. PLoS Comput Biol, 11(2):1–28, 02 2015.

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Published

2019-03-01

How to Cite

Brodnik, A., Jovičić, V., Palangetić, M., & Silađi, D. (2019). Construction of orthogonal CC-sets. Informatica, 43(1). https://doi.org/10.31449/inf.v43i1.2693

Issue

Vol. 43 No. 1 (2019)

Section

Middle-European Conference on Applied Theoretical Computer Science (MATCOS-16)

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