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Abstract: In this paper, we give a comprehensive overview of the development of clique algo-rithms and their use for drug design based on the search for cliques in protein productgraphs. The maximum clique problem is a computational problem of finding largest sub-sets of vertices in a graph that are all pairwise adjacent. A related problem is the maximumweight clique problem and the highest weight k-clique problem, which both extend the al-gorithm to weighted graphs. The review covers our developed algorithms, starting with ourimproved branch-and-bound algorithm for finding maximum cliques in undirected graphsfrom 2007 up to the recent developments of algorithms for weighted graphs in 2024. Weshow the application of these algorithms to early stages of drug discovery, in particular toprotein binding site detection based on protein similarity search in large protein databasesand to protein-ligand molecular docking.
Keywords: cliques, protein product graphs, applications
Published in RUP: 08.08.2025; Views: 958; Downloads: 15
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