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OpenSMOG - This is an OpenMM library that provides integrated support for SMOG models, and it is part of the SMOG set of tools supported by the Whitford and Onuchic Groups. With the design structure of OpenMM, OpenSMOG allows one to use SMOG2 to construct more creative versions of SMOG models. The lead developers are Antonio Martins and Vinicius Contessoto.
RADtool - The Ribosome Analysis Database is driven by RADtool. This is a Tcl-based plugin for VMD that can be used to retrieve and analyze ribosome structures. The plugin can identify subunits, align them to a common references, identify structurally-conserved regions, calculate rotation angles, and more. The software may be used via the command line, or one may use the GUI (recommended in most cases). This tool provides a systematic framework for the analysis and comparison of ribosome structures. RADtool was developed by the Whitford Group.
openAWSEM - An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM. openAWSEM is the last iteration of the AWSEM forcefield family, which is being developed by the Wolynes group. There is a iteration in LAMMPS that is still being used http://awsem-md.org/. The lead developers are Wei Lu and Nick Schafer with collaboration of other members of the Wolynes group.
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