20.500.12556/RUL-155379 Enhanced molecular docking novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs Molecular docking, a key process in drug discovery, is often used in the discovery of new bioactive compounds. In this technique, small molecules are systematically placed at a protein binding site to identify the ligands with the highest binding affinity. Here we have developed a new graph-theoretical algorithm called K-CliqueWeight. This algorithm efficiently identifies the top N highest weight k-cliques in different types of vertex-weighted graphs and can serve as a building block for various algorithms addressing different problems, including molecular docking. K-CliqueWeight and its variant K-CliqueDynWeight are extensions of our established and widely used maximum clique algorithm. Our new algorithm uses a novel approach to approximate graph coloring and provides efficient upper bounds on the size and weight of a k-clique within the branch-and-bound algorithm. It outperforms alternative methods and often shows a speedup of several orders of magnitude. Rigorous tests with general random graphs and those specifically designed for docking confirm its exceptional performance. K-CliqueWeight has been integrated into the existing ProBiS-Dock algorithm for molecular docking. The algorithm is freely available to the academic community at http://insilab.org/kcliqueweight. highest weight k-cliques algorithm weighted graphs graph coloring graph theory molecular docking ProBiS-Dock algorithm molekularna biologija bioaktivne sestavine zdravila ligandi vezavna mesta algoritmi true false true Angleški jezik Slovenski jezik Članek v reviji 2024-03-28 10:04:27 2024-03-28 10:04:28 2024-05-28 08:30:02 0000-00-00 00:00:00 2024 0 0 10 str. art. 137639 Vol. 1304 2024 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 577 1872-8014 10.1016/j.molstruc.2024.137639 182995715 1-s2.0-S0022286024001625-main.pdf 1-s2.0-S0022286024001625-main.pdf 1 ACB523532ADC59F868F0728DEADC8E46 13c9ea80941f3510d174b7e95244643b7621d00abb384c86fc9dedcf49386557 16df1a93-ece4-11ee-a8ca-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=182233 https://www.sciencedirect.com/science/article/pii/S0022286024001625 1 2fcdee91-ece2-11ee-a8ca-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=182232 Biotehniška fakulteta Fakulteta za farmacijo 0 0 0