Abstract

Computer-aided drug design (CADD) is a generic term for powerful computational tools that include a diverse set of methodologies routinely used by pharmaceutical scientists to help develop the best viable drug candidates. The use of protein structures as the starting point in drug discovery is often called structure-based drug design (SBDD). The protein structures used in molecular modeling generally come from three sources of detailed three-dimensional (3D) data: (a) X-ray crystallography, (b) nuclear magnetic resonance (NMR) spectroscopy, and (c) homology modeling. The first two methods generate structures that are based on experiments, whereas homology modeling involves the use of computational methods. An important development in SBDD has been in silico derived structures. Electron microscopy is another source of experimentally generated structures, but the number of structures from electron microscopy in the ProteinData Bank (PDB) is quite small compared with the other methods. For example, only 371 out of 74,297 entries are listed as of July 5, 2011, which is less than 0.5% of the deposited entries in the PDB. Therefore, the focus of the following discussion will be on structures determined by X-ray, NMR, and homology modeling.