AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
The flexibility information of the ligand (i.e. rotatable bonds) and receptor (i.e. flexible side-chains) is used to assemble the genome from which an initial list of solutions (i.e. population) is created. The population is scored, sorted, and top-ranking solutions are clustered. The GA seeds the next generation with the best solution of each cluster and completes it by crossing-over, mutating, and minimizing individuals from the mating population. The optimization stops when one of the termination criteria (maximum number of generations or evaluations) is reached or the search converges, at which point the solutions within 1 kcal/mol of the best solution are written out.