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In our method, the seam is selected by both energy function and main content protection.
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Both RW and HC use the same energy function and transition function as SA.
The current work presents our motivation for deriving such an energy function and also tests the derived energy function.
So, it is necessary to make protein-ligand potential energy function and scoring function more accurate.
To fairly evaluate FRazor, we used ROSETTA's energy function and its default setting.
We call function η the energy function, and any circular ordering that minimizes η is called the optimal circular ordering.
Insertion of backbone fragments rapidly "folds" the protein using the low-resolution energy function and sampling approaches.
The largest eigenvalue, λ1, is close to 50% for both energy functions.
OSCAR-o, which uses both orientation-dependent energy functions and a flexible roamer model, is the most accurate and also slower than the other methods.
A more general approach would allow for different free energy functions (and thus two different χ) in both monolayers.
Our results indicate that the classical particle swarm optimization with constant cognitive and social parameters is a reliable method and offers the best performance for global minimization of the tangent plane distance function and the Gibbs energy function in both reactive and non-reactive systems.
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