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Modelfree


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OS: Linux, Mac

License: Freeware





Modelfree (version 4.0) is a program to fit the extended model free spectral density function to NMR spin relaxation data. The program can analyze the spin-lattice relaxation rate constant (R1), the spin-spin relaxation rate constant (R2), and the heteronuclear steady-state {1H}-X nuclear Overhauser effect (NOE) for any combination of 13C and 15N spins at up to five static magnetic fields. The algorithm assumes dipolar and chemical shift anisotropy (CSA) relaxation mechanisms for R1, R2 and the NOE and includes an additive term to account for chemical exchange broadening of R2. The exchange broadening parameter is scaled quadratically with respect to the static magnetic field if data for more than one field is available.

Modelfree incorporates three models for rotational diffusion. Brent's method is used to optimize a single global ?m for an isotropic overall diffusion model. Either Powell's method (as implemented by Brent) or a simulated annealing protocol (based on the downhill simplex method) is used to optimize a global rotational diffusion tensor for an axially symmetric diffusion model. A local rotational correlation time, ?mi, for each spin can be optimized by non-linear least squares regression.

Other internal model free parameters (order parameters, internal correlation times and chemical exchange terms) are optimized by restrained non-linear least squares. Any parameter can be fixed at its input value rather than optimized and simple bounds can be placed on any parameter. Monte Carlo simulations are used to estimate uncertainties in model-free parameters and to perform statistical model selection based on F-testing.

http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/modelfree.html



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