Supplemental Data
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
Software
cosmo_psi4
Description:scosmo implicit solvation reference implementation as a psi4 plugin
Author(s): T.J. Giese, Darrin M. York
License: LGPL
Dependencies: PSI4
Citation: T.J. Giese, E.R. Kuechler, D.M. York, "Implementation of the smooth conductor-like solvation model"
tdbsc
Description:Implementation of a sugar pucker correction via 2d B-spline interpolation of pretabulated data
Author(s): T.J. Giese, Darrin M. York
License: MIT
Downloads: Source Code
Dependencies: fftw3
Citation:
M. Huang, T. J. Giese, T.-S. Lee and D. M. York, "Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods", J. Chem. Theory Comput., (2014) 10, 1538-1545
vFEP
Description:Used to obtain a free energy profile from a set of umbrella sampling simulations
Author(s): T.S. Lee, Darrin M. York
License: GPL
Webpage:
Downloads: Source Code
Dependencies: alglib dlib
Citation:
Lee, T.S., Radak, B..K.; Pabis A.; York, D. M., “A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations”, J. Chem. Theory Comput. 2013, 9:153