Figure 1.

Sketch map of data structure in LigBuilder V3. (A) The overview structure of GA evolution and GA compound pool. The GA compound pool includes the ensemble of molecules evolved in GA population. For multi-target design, conformations for each receptor are listed in corresponding column, as a result, each row could represent a solution of multi-target inhibition, and it could be viewed as the basic unit in multi-target GA population, which has similar status as “molecule” in single-target GA population. To avoid confusion, we define each row as a “conformation group” instead of “molecule” or “conformation.” (B) The definition of chemical cluster and conformation cluster. The compound pool is clustered on two levels: (a) all molecules sharing identical chemical structures will be clustered as chemical cluster, which could be synthesized by same route; (b) conformations with similar protein-ligand interaction will be clustered as conformation cluster, which represent same interaction mode.