Using finite element simulations and analyzing test data, we verified that our modeling approach was correct and provided a valid foundation for further calculations.
Displacement of retained water molecules in the distal site was considered by performing classical MD simulations and analyzing the solvation structure in each active site.
We compared γ-MYN with two other methods, YN and MYN, by examining long sequences, performing computer simulations, and analyzing real datasets.
We compared MYN with other methods, especially with YN, by examining infinitely long sequences, performing computer simulations and analyzing real datasets, and found that MYN has minimal deviation even when parameters vary within normal ranges defined by empirical data.
All authors contribute to the development and implementation of the algorithms, and FY and JT are in charge of conducting simulations and analyzing results.
This allows the user to exploit the interactive features and visualization tools of MATLAB for setting up simulations and analyzing and interpreting the resulting data.
