nmr relax
Details
| Last Update: | 2008-04-21 01:24:54 |
| Version: | nmr-relax 1.2.13 |
| License/Program Type: | GPL (GNU General Public License) |
| Publisher: | Edward d\'Auvergne |
| Price: | $0.00 |
Description:
nmr-relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. It is a community driven project created by NMR spectroscopists for NMR spectroscopists.
It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis.
Here are some key features of "nmr relax":
Supported NMR theories
· The following relaxation data analysis techniques are currently supported by relax:
· Model-free analysis (Lipari and Szabo, 1982a; Lipari and Szabo, 1982b; Clore et al., 1990)
· Reduced spectral density mapping (Farrow et al., 1995, Lefevre et al., 1996)
· Exponential curve fitting (to find the R1 and R2 relaxation rates)
· Steady-state NOE calculation
Data analysis tools
The following tools are implemented as modular components to be used by any data analysis technique:
· Numerous high-precision optimisation algorithms
· Model selection (d'Auvergne and Gooley, 2003)
· Akaike's Information Criteria (AIC)
· Small sample size corrected AIC (AICc)
· Bayesian or Schwarz Information Criteria (BIC)
· Bootstrap model selection
· Single-item-out cross-validation (CV)
· Hypothesis testing ANOVA model selection (only the model-free specific technique of Mandel et al., 1995 is supported)
· Monte Carlo simulations (error analysis for all data analysis techniques)
· Model elimination - the removal of failed models prior to model selection (d'Auvergne and Gooley, 2006)
Requirements:
·
What's New in 1.3.0 Development Release:
· New features include the addition of a unit test framework, preliminary support for PyMOL, the creation of PDB files, the ability to display the diffusion tensor as a geometric object through a PDB file using PyMOL, and the ability to display the distribution of XH bond vectors used in the analysis via a PDB file.
What's New in 1.2.13 Stable Release:
· The addition of the consistency testing of relaxation data from different field strengths using the J(0), F_eta, and F_R2 values as calculated in Fushman et al., (1998) JACS, 120, 10947-10952.
· Important bugs have been fixed, including the failure of Monte Carlo simulations when the model-free model 'm0' is encountered causing the parameter errors for all subsequent residues to be zero, the failure of reading of Art Palmer's Modelfree 4 'mfout' file, and the handling of missing structural data.
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