An evolutionary approach for molecular docking

We have developed an evolutionary approach for the flexible docking that is now an important component of a rational drug design. This automatic docking tool, referred to as the GEMDOCK (Generic Evolutionary Method for DOCKing molecules), combines both global and local search strategies search mechanisms. GEMDOCKused a simple scoring function to recognize compounds by minimizing the energy of molecular interactions. The interactive types of atoms between ligands and proteins of our linear scoring function consist only hydrogen-bonding and steric terms. GEMDOCK has been tested on a diverse dataset of 100 protein-ligand complexes from Protein Data Bank. In total 76% of these complexes, it obtained docked ligand conformations with root mean square derivations (RMSD) to the crystal ligand structures less than 2.0 Å when the ligand was docked back into the binding site. Experiments shows that the scoring function is simple and efficiently discriminates between native and non-native docked conformations. This study suggests that GEMDOCK is a useful tool for molecular recognition and is a potential docking tool for protein structure variations.