Advanced clique algorithms for protein product graphs

Résumé fourni par la source

In this paper, we give a comprehensive overview of the development of clique algorithms and their use for drug design based on the search for cliques in protein product graphs. The maximum clique problem is a computational problem of finding largest subsets of vertices in a graph that are all pairwise adjacent. A related problem is the maximum weight clique problem and the highest weight k-clique problem, which both extend the algorithm to weighted graphs. The review covers our developed algorithms, starting with our improved branch-and-bound algorithm for finding maximum cliques in undirected graphs from 2007 up to the recent developments of algorithms for weighted graphs in 2024. We show the application of these algorithms to early stages of drug discovery, in particular to protein binding site detection based on protein similarity search in large protein databases and to protein-ligand molecular docking.

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