RADtool

RADtool is a plugin for VMD that allows for analysis and visualization of ribosomes from all domains of life. Specifically, this tool will align almost any ribosome to a reference E. coli structure, find the structurally-conserved residues and then quantify the orientations of the head and body domains of the small subunit.

RADtool is used to generate the Ribosome Analysis Database. By applying this tool, we have been able to systematically catalogue more than 2000 published structures. This database is updated daily, so newly-released ribosome structures often appear in the RAD database within a day.

RADtool provides a direct method for comparing almost any ribosome structure. It can be used to analyze structures in RCSB, or it can be used to analyze unpublished structures. In addition, we have found that the combined tool-database are very well suited for training new ribosome researchers (e.g. new grad students).