While the RADtool software allows each user to interactively assess the domain orientations of any ribosome structure in VMD, it can still be challenging to compare a new structure to the 1000+ structures that have been published. To this end, we provide web-based tools for querying and comparing with published structures. These tools draw statistics from the current Ribosome Analysis Database, which is regularly updated.

Database Query Tool

This tool allows one to search all ribosome structures (full ribosomes, isolated SSUs or isolated LSUs) that are in the database. There are various search options, including specifying rotation angle ranges (Euler angles), organism names, publication information and more.

Find Similar Structures Tool

With this tool, you specify an orientation (in terms of the angles calculated by RADtool, or by RCSB ID) and it will calculate the angular proximity of every structure in the RCSB database. One may then compare structures based on SSU head or SSU body orientations. This tool is most helpful for comparing unpublished structures with all published structures. For that purpose, you would first use RADtool to analyze your structure, then use this search tool to determine if there are any published structures that are similar.

Compare Two Tool

Since RAD angles represent a complete coordinate system for describing the orientations of the SSU body and head, they may be used to quantitatively compare arbitrary structures. This tool will use RAD angles to determine the relative tilt difference and Euler-Rodrigues angles between any two ribosome structures. This tool is most useful if you generate RAD angles for two unpublished structures. The differences between the orientations may then be compared with this tool.

Page created and maintained by the Whitford Group at the Center for Theoretical Biological Physics, Northeastern University.