We construct an undirected graph in which vertices represent seed fragments, and edges indicate that the corresponding pair of seed fragments is linkable. Using the MaxCliqueDyn algorithm of Konc and Janezic 34 , we then find all fully connected subgraphs consisting of k vertices (k-cliques) in this graph, where the default value of k is set to three or to the number of seed fragments, whichever value is less. Each k-clique corresponds to a possible partial conformation of the docked seed fragments, in which these fragments are appropriately distanced so that they may be linked into the original compound. The possible partial conformations are then clustered using a greedy clustering algorithm at RMSD cutoff of 2 Å, where the best-scored cluster representatives are retained. The partial conformations sorted by their RMR6 scores from the best-to the worst-scored are used as an input to the next step of compound reconstruction.