Relevant Literature

• A. Hassan, S. Byju, F. C. Freitas, C. Roc, N. Pender, K. Nguyen, E. M. Kimbrough, J. Mattingly, R. L. Gonzalez Jr., R. J. de Oliveira, C. M. Dunham, P. C. Whitford. Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome. 2022. Nucleic Acids Research. DOI: 10.1093/nar/gkac1211

  The RADtool software and algorithms are described in this manuscript. It describes refined definitions of rotation angles, as well as robust protocols that allow for the analysis of rotation and translational displacements in nearly any ribosome structure. All quantities in the database were generated with RADtool.

Earlier algorithms
The methods implemented in RADtool have been developed over years, and elements have been discussed in various manuscripts. Here are some key references:

• K. Nguyen, P. C. Whitford. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nature Communications. 7, 10586, 2016. link

  This is the first manuscript in which we used Euler angles to describe rotation of the SSU head in bacteria.

• F. Campos Freitas, G. Fuchs, R. J. de Oliveira, P. C. Whitford. The dynamics of subunit rotation in a eukaryotic ribosome. Biophysica, 1, 204-221, 2021. link

  This manuscript describes an earlier Euler angle based protocol that allowed for the calculation of rotation and tilt angles in eukaryotic ribosomes.

Graphics
On this page, structures in the banner show RCSB ID 3J77 and 4V6F, as well as a snapshot from simulations of hybrid formation.

Software Registry Information
The Ribosome Angle Decomposition Tool (RADtool) - RRID:SCR_022550

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