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) and
Ribosome Analysis Database
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. This approach provides a complete description of any ribosomal subunit. Since calculating rigid-body rotations can be quite complex, we have prepared a VMD plugin (called RADtool) that will calculate the tilt angle, tilt direction and rotation angle for the 30S head and body, given a PDB structure. RADtool can analyze essentially any structure of a ribosome, as well as generate visualizations for comparative analysis of any two ribosome structures. To demonstrate the power of this software, it is used to drive the Ribosome Analysis Database, which provides a complete list of ribosome structures (over 1800 structures, as of June 2022), along with orientation descriptors. To access the database, or use the tool, see the Ribosome Analysis Database page.