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We present a depth-first search algorithm for generating all maximal cliques of an undirected graph, in which pruning methods are employed as in the Bron–Kerbosch algorithm. All the maximal cliques generated are output in a tree-like form. Subsequently, we prove that its worst-case time complexity is O(3 n/3) for an n-vertex graph. This is optimal as a(More)
SUMMARY Many problems can be formulated as maximum clique problems. Hence, it is highly important to develop algorithms that can find a maximum clique very fast in practice. We propose new approximate coloring and other related techniques which markedly improve the run time of the branch-and-bound algorithm MCR (J. Global Optim., 37, pp.95–111, 2007),(More)
"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum(More)
BACKGROUND Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, including diseases. There is thus a strong need for a way to automatically and comprehensively search from biomedical databases for related(More)
With the advent of experimental technologies like chemical cross-linking, it has become possible to obtain distances between specific residues of a newly sequenced protein. These types of experiments usually are less time consuming than X-ray crystallography or NMR. Consequently, it is highly desired to develop a method that incorporates this distance(More)