GEMDOCK is a nearly automatic tool for virtual screening. GEMDOCK can sequentially be applied to four computational phases, including target and database preparation, molecular docking and post-docking analysis. First we specified the coordinates of target protein atoms from the PDB, the ligand binding area, atom formal charge and atom types. Second GEMDOCK is able to sequentially read the atom coordinates of a ligand from the prepared ligand database. After GEMDOCK prepares the ligand database and the target protein, it sequentially executes flexible docking for each ligand. Finally GEMDOCK re-ranks and sorts all docked ligand conformations for the post-docking analysis.
GEMDOCK uses an empirical scoring function and an evolutionary approach. The GEMDOCK energy function consists of electrostatic, steric, and hydrogen-bonding potentials. The latter two terms use a linear model that is simple and recognizes potential complexes rapidly. The core idea of this evolutionary approach is to design multiple operators that cooperate using a family competition paradigm that is similar to a local search procedure.