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DynaMut is a user friendly web server that implements two distinct well established normal mode approaches, which can be used to analyse protein dynamics by sampling conformations as well as assess the impact of mutations on protein stability and dynamics.
To study the dynamic nature and the role of flexibility/rigidity and accessible conformational landscapes in proteins is essential for understanding their function, as well as to evaluate how changes in a protein might impact its structure, function and interactions, giving rise to different phenotypes.
On the analysis submission page:
|C-alpha||Force field derived from fitting to the Amber94 all-atom potential.|
|ANM||Anisotropic Network Model uses a simplified spring force constant based on the pair-wise distance.|
|pfANM||parameter-free Anisotropic Network Model is variant from the ANM force field with interactions that fall off with the square of the distance.|
|REACH||Realistic Extension Algorithm via Covariance Hessian is parameterized based on variance-covariance matrices obtained from MD simulations.|
|sdENM||This force field employs residue specific spring force constants and it has been parameterized through a statistical analysis of 1500 NMR ensembles.|
On the first section of the analysis results page:
On the second section of the analysis results page:
On the third section of the analysis results page:
On the Residue Cross-Correlation tab (1):
On the prediction submission page:
The results for a single mutation will be displayed once computations are completed in 3 different panels. On the first tab, ΔΔG Predictions (1):
The second tab, Interatomic Interactions (1):
The third tab, Deformation and Fluctuation Analysis (1):
The results for a list of mutations will be displayed in a table format with the following information:
In case you experience any trouble using Dynamut or have any suggestions or comments, please do not hesitate in contacting us either via e-mail (1) or through the online form (2) .