In order to increase accessibility of computational methods employed by the group, we provide support for open-source software that allows for the simulation and analysis of biomolecular systems.

SMOG-SERVER, SMOG2 and OpenSMOG

The Noel-Onuchic-Whitford class of structure-based models are available at smog-server.org. smog-server has both a web interface (smog 1), as well as a more versatile standalone version (smog 2, highly recommended) and an interface for OpenMM (called OpenSMOG). If you find these tools are limited, let us know. All tools may be accessed through the smog-server page. We are constantly expanding the support provided, in order to help researchers address the most challenging biophysical questions.

The Ribosome Angle Decomposition Tool (RADtool)

We have been very interested in developing systematic measures of subunit rotation in ribosomes. In order to unambiguously define any rigid body rotations and translations, we use Euler Angles (as initially described in Nguyen and Whitford, 2016 and expanded later). Since calculating rigid-body rotations can be quite complex, we have prepared a VMD plugin that will calculate the tilt angle, tilt direction and rotation angle for the 30S head and body, given a PDB structure. We plan to release this software in March 2022, at which time full documentation will be available. However, if you are interested in beta testing it, let us know.