Protein Structure Comparison Maximum Clique K-Partite Graphs Integer Programming Branch and Bound
Institute of Mathematics and Informatics Bulgarian Academy of Sciences
Serdica Journal of Computing, Vol. 4, No 1, (2010), 93p-100p
Computing the similarity between two protein structures is
a crucial task in molecular biology, and has been extensively investigated.
Many protein structure comparison methods can be modeled as maximum
weighted clique problems in specific k-partite graphs, referred here as alignment graphs.
In this paper we present both a new integer programming formulation
for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches
have been integrated in VAST, a software for aligning protein 3D structures
largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm
(BK). Our computational results on real protein alignment instances show
that our branch and bound algorithm is up to 116 times faster than BK.