Molecular Modeling - Seeing the Whole Picture with Modeling Software Packages

Date: August 31, 1998Table 1: Molecular Modeling Software, Table 2: Structure & Modeling Information and Table 3: Visualization & Image Resources The term "molecular modeling" usually conjures up two images: three-dimensional (3-D) depictions of small molecular structures (for example, benzene) and biological macromolecular structures (for example, proteins, DNA, and RNA). Some of the earliest and perhaps most renowned 3-D representations of a biological macromolecule were the wire-frame and paper models of deoxyribonucleic acid developed by James Watson and Francis Crick, who used this physical modeling technique to decipher the arrangement of deoxyribonucleotides in the DNA "double helix" (J.D. Watson, "The Double Helix," Antheneum, 1968). Within the next decade, computational tools had made their way into molecular structure analysis. Although crude by today's standards, these tools contributed to the structural analyses of cytochrome c and myoglobin. For an interesting historical perspective, read Cyrus Levinthal's "Molecular Model Building by Computer" (Scientific American, ...