ABSTRACT
Computers are an integral part of the drug design process and have a large number of applications, which include structure analysis, structure comparisons, lead compound design, identification of active conformations and pharmacophores, combinatorial library design, protein and binding site structure, ligand binding, Quantitative structure–activity relationships (QSAR) and three dimensions (3-D) QSAR. Molecular modeling software allows the medicinal chemist to create a model of a compound in 3D. Once two compounds have been converted to their 3-D structures, molecular modeling can be used to compare how similar they are in structure. The molecules can be overlaid by identifying pairs of atoms where one atom of each atom pair belongs to one structure and the other atom is considered to be its equivalent in the second structure. Once the interactions of the ligand with the binding site have been studied, the ligand can be ‘removed’ to leave the empty site.
