Constant coefficients of diffusion were set in the DICTRA macro using the command "ENTER_MOBILITY_ESTIMATE". The coefficient of diffusions and equilibrium concentrations were therefore the same in the mixed-mode calculation and the DICTRA simulation.
Here, we call this series of calculations "iterative normal-mode calculation" and use this approach for forcing the conformational change of integrin from the bent to the extended forms and studying the role of the specific interactions in the conformational change.
We deformed the x-ray crystal structure of integrin by iterative normal-mode calculations and studied the impact of eliminating the interactions we found above on the global conformational change from the bent to the extended forms.
A subsequent suggestion that closure of the hydrophobic groove produced GDP expulsion [18] was itself later seen to be inconsistent, first with our own normal mode calculations [34] and then more directly with the crystal structures of the BFA-blocked complex (intermediate I) in which the hydrophobic groove was closed but the nucleotide remained in place [6], [19].
All these details are provided in the output of single chemical and batch mode calculation.
We show how this impedance condition can be implemented in a mode calculation method by introducing auxiliary variables.
To describe the nonlinearity of the conformational changes during protein unfolding, a method based on the iterative use of normal mode calculation is proposed.
The present note illustrates a criterion to improve the computational capability of the approaches proposed by Beltrami et al. [Beltrami, G.M., Bargagli, A., Briganti, R., 2003. Gravitational mode calculation of basins discretised by orthogonal curvilinear grids.
Mode calculation is formulated as an iterative scheme of mean calculation, which takes a certain number of feature points and calculates their weighted mean value by using a kernel function, such as the Gaussian.
NEEMP is implemented as a single C program which switches among its three modes (calculation, parameterization, and validation) according to a command line option.
