Smith Lab Software
FitNMR
FitNMR is an R package that does multidimensional NMR peak fitting. It enables quantification of highly overlapped peaks and extraction of parameters like R2 rates and unresolved scalar couplings.
Documentation – Download Releases – Source Code on GitHub
Kinetic Ensemble Refinement (KER)
We are in the process of developing an open-source implementation of the Kinetic Ensemble method for back-calculating NOE relaxation rates and intensities, as well as generating coordinate restraints on the fly during ensemble refinement calculations. These will be released as a C++ library using a permissive open-source license compatible with nearly all biomolecular modeling software, as well as being integrated into an R package.
Rosetta Biomolecular Modeling Suite
The Smith Lab is a member of the Rosetta Commons, helping steer development of the Rosetta software suite for macromolecular modeling and design. It is extensively used in both academia and industry. We regularly attend the summer and winter annual meetings. Colin Smith is one of the organizers of the 2021 annual summer meeting and will be a member of the Executive Board (as Membership Chair) starting in the fall of 2021.
Documentation – Download Releases
Computational Resources
Wesleyan High Performance Computing Cluster
Wesleyan University runs a shared High-Performance Computing (HPC) cluster that has a mix of CPU-only and CPU/GPU nodes. Our most demanding jobs use the Gromacs molecular dynamics simulation software, which has been written to take advantage of the massive computational power of consumer-level Graphics Processing Unit (GPU) cards originally designed for playing video games. This enables us to run large and/or long simulations at a fraction of the time and cost that would otherwise be required.
National Science Foundation XSEDE Supercomputers
We also use the National Science Foundation (NSF) Extreme Science and Engineering Discovery Environment (XSEDE) for our computer simulations. We have received allocations to support molecular dynamics simulations of Superoxide Dismutase 1 (SOD1) maturation. We have also used XSEDE supercomputers for the Molecular Modeling & Design course taught by Prof. Smith.
NMRBox
NMRBox hosts a large repository of software for analyzing NMR data. It is deployed on a set of virtual machines that users can log into from all over the world and run both graphical and command line software. NMRBox is run by the University of Connecticut Health Center, which is about half an hour away from Wesleyan University.