Here, we present protocols for using two common visualization tools-the Web-based Jmol and the stand-alone PyMOL package-as well as a few examples of other popular tools. More detailed information about the Protein Data Bank and PDB files will be discussed within the Jmol Training Guide Part II. In order for the researcher to take advantage of such a wealth of structural data, it is necessary to gain competency in the use of computer molecular visualization tools for exploring the structures and visualizing three-dimensional spatial representations. Furthermore, these structural snapshots serve as inputs for sophisticated computer simulations to turn the biomolecules into moving, “breathing” molecular machines for understanding their dynamic properties in real-time computer simulations. Rastop (Windows machines) and Jmol(platform-independent server-side java viewer). These snapshots can help explain how the biomolecules function, the nature of interactions between multi-molecular complexes, and even how small-molecule drugs can modulate the biomolecules for clinical benefits. examination of a protein structure for similarity with the whole PDB. the structure files were imported into Jmol and modified into Active site of HIV Protease. An enormous amount of structural data for a large number of these biomolecules has been described with atomic precision in the form of structural “snapshots” that are freely available in public repositories. PDB IDs: Overlay1 of wild-type (2HU4) and H274Y mutant (3CL0). Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms.

Jmol overlay pdb